From e3eabfe6db5a2dd6beb4bbaffa092536474fc9b8 Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Mon, 5 Jun 2023 11:34:51 +0200 Subject: [PATCH 01/34] Init for the no listing workflow --- cwltool.code-workspace | 8 + cwltool/argparser.py | 18 + cwltool/cwlprov/__init__.py | 36 +- cwltool/cwlprov/provenance_profile.py | 3 + cwltool/cwlprov/ro.py | 39 +- cwltool/executors.py | 2 +- cwltool/job.py | 3 +- cwltool/main.py | 23 +- tests/test_provenance.py | 127 + ...nce.py::test_directory_workflow_no_listing | 32987 ++++++++++++++++ tests/wf/directory_no_listing.cwl | 79 + 11 files changed, 33309 insertions(+), 16 deletions(-) create mode 100644 cwltool.code-workspace create mode 100644 tests/test_provenance.py::test_directory_workflow_no_listing create mode 100644 tests/wf/directory_no_listing.cwl diff --git a/cwltool.code-workspace b/cwltool.code-workspace new file mode 100644 index 000000000..876a1499c --- /dev/null +++ b/cwltool.code-workspace @@ -0,0 +1,8 @@ +{ + "folders": [ + { + "path": "." + } + ], + "settings": {} +} \ No newline at end of file diff --git a/cwltool/argparser.py b/cwltool/argparser.py index 5439d2bd2..60050ff5e 100644 --- a/cwltool/argparser.py +++ b/cwltool/argparser.py @@ -287,6 +287,24 @@ def arg_parser() -> argparse.ArgumentParser: type=str, ) + # TO DO: Not yet implemented + provgroup.add_argument( + "--no-data", # Maybe change to no-input and no-intermediate to ignore those kind of files?... + default=False, + action="store_true", + help="Disables the storage of input and output data files of the workflow in the provenance data folder", + dest="no_data", + ) + + # TO DO: Not yet implemented + provgroup.add_argument( + "--no-input", # Maybe change to no-input and no-intermediate to ignore those kind of files?... + default=False, + action="store_true", + help="Disables the storage of input and output data files of the workflow in the provenance data folder", + dest="no_input", + ) + printgroup = parser.add_mutually_exclusive_group() printgroup.add_argument( "--print-rdf", diff --git a/cwltool/cwlprov/__init__.py b/cwltool/cwlprov/__init__.py index 98e8c911c..78663ae4c 100644 --- a/cwltool/cwlprov/__init__.py +++ b/cwltool/cwlprov/__init__.py @@ -10,6 +10,9 @@ from typing_extensions import TypedDict +from cwltool.cwlprov.provenance_constants import Hasher + +from ..loghandler import _logger def _whoami() -> Tuple[str, str]: """Return the current operating system account as (username, fullname).""" @@ -135,7 +138,7 @@ def _valid_orcid(orcid: Optional[str]) -> str: def checksum_copy( src_file: IO[Any], dst_file: Optional[IO[Any]] = None, - hasher: Optional[Callable[[], "hashlib._Hash"]] = None, + hasher=Hasher, # type: Callable[[], hashlib._Hash] buffersize: int = 1024 * 1024, ) -> str: """Compute checksums while copying a file.""" @@ -158,6 +161,35 @@ def checksum_copy( pass if os.path.exists(temp_location): os.rename(temp_location, dst_file.name) # type: ignore + + return content_processor(contents, src_file, dst_file, checksum, buffersize) + + +def checksum_only( + src_file: IO[Any], + dst_file: Optional[IO[Any]] = None, + hasher=Hasher, # type: Callable[[], hashlib._Hash] + buffersize: int = 1024 * 1024, +) -> str: + """Calculate the checksum only, does not copy the data files.""" + if dst_file is not None: + _logger.error("Destination file should be None but it is %s", dst_file) + """Compute checksums while copying a file.""" + # TODO: Use hashlib.new(Hasher_str) instead? + checksum = hasher() + contents = src_file.read(buffersize) + # TODO Could be a function for both checksum_only and checksum_copy? + return content_processor(contents, src_file, dst_file, checksum, buffersize) + + +def content_processor( + contents: Any, + src_file: IO[Any], + dst_file: Optional[IO[Any]], + checksum: "hashlib._Hash", + buffersize: int, +) -> str: + """Calculate the checksum based on the content.""" while contents != b"": if dst_file is not None: dst_file.write(contents) @@ -165,4 +197,4 @@ def checksum_copy( contents = src_file.read(buffersize) if dst_file is not None: dst_file.flush() - return checksum.hexdigest().lower() + return checksum.hexdigest().lower() \ No newline at end of file diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index ad019f3e5..f9ff5ee9f 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -243,6 +243,7 @@ def evaluate( # record provenance of workflow executions self.prospective_prov(job) customised_job = copy_job_order(job, job_order_object) + # Note to self: Listing goes ok here self.used_artefacts(customised_job, self.workflow_run_uri) def record_process_start( @@ -287,6 +288,7 @@ def record_process_end( process_run_id: str, outputs: Union[CWLObjectType, MutableSequence[CWLObjectType], None], when: datetime.datetime, + # load_listing: None, ) -> None: self.generate_output_prov(outputs, process_run_id, process_name) self.document.wasEndedBy(process_run_id, None, self.workflow_run_uri, when) @@ -604,6 +606,7 @@ def used_artefacts( job_order: Union[CWLObjectType, List[CWLObjectType]], process_run_id: str, name: Optional[str] = None, + load_listing = None, ) -> None: """Add used() for each data artefact.""" if isinstance(job_order, list): diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 3bcc9fddf..f819113e9 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -34,7 +34,7 @@ posix_path, versionstring, ) -from . import Aggregate, Annotation, AuthoredBy, _valid_orcid, _whoami, checksum_copy +from . import Aggregate, Annotation, AuthoredBy, _valid_orcid, _whoami, checksum_copy, checksum_only from .provenance_constants import ( ACCOUNT_UUID, CWLPROV_VERSION, @@ -66,6 +66,7 @@ def __init__( temp_prefix_ro: str = "tmp", orcid: str = "", full_name: str = "", + no_data: bool = False, ) -> None: """Initialize the ResearchObject.""" self.temp_prefix = temp_prefix_ro @@ -88,6 +89,7 @@ def __init__( self.cwltool_version = f"cwltool {versionstring().split()[-1]}" self.has_manifest = False self.relativised_input_object: CWLObjectType = {} + self.no_data = no_data self._initialize() _logger.debug("[provenance] Temporary research object: %s", self.folder) @@ -180,13 +182,22 @@ def add_tagfile(self, path: str, timestamp: Optional[datetime.datetime] = None) # Below probably OK for now as metadata files # are not too large..? - checksums[SHA1] = checksum_copy(tag_file, hasher=hashlib.sha1) + if self.no_data: + _logger.warning("NO DATA TO BE CAPTURED!!!") - tag_file.seek(0) - checksums[SHA256] = checksum_copy(tag_file, hasher=hashlib.sha256) + checksums[SHA1] = checksum_only(tag_file, hasher=hashlib.sha1) + tag_file.seek(0) + checksums[SHA256] = checksum_only(tag_file, hasher=hashlib.sha256) + tag_file.seek(0) + checksums[SHA512] = checksum_only(tag_file, hasher=hashlib.sha512) + else: + checksums[SHA1] = checksum_copy(tag_file, hasher=hashlib.sha1) + + tag_file.seek(0) + checksums[SHA256] = checksum_copy(tag_file, hasher=hashlib.sha256) - tag_file.seek(0) - checksums[SHA512] = checksum_copy(tag_file, hasher=hashlib.sha512) + tag_file.seek(0) + checksums[SHA512] = checksum_copy(tag_file, hasher=hashlib.sha512) rel_path = posix_path(os.path.relpath(path, self.folder)) self.tagfiles.add(rel_path) @@ -469,10 +480,14 @@ def add_data_file( content_type: Optional[str] = None, ) -> str: """Copy inputs to data/ folder.""" + # TODO Skip if no-input or no-data is used...? self.self_check() tmp_dir, tmp_prefix = os.path.split(self.temp_prefix) with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp: - checksum = checksum_copy(from_fp, tmp) + if self.no_data: + checksum = checksum_only(from_fp) + else: + checksum = checksum_copy(from_fp, tmp) # Calculate hash-based file path folder = os.path.join(self.folder, DATA, checksum[0:2]) @@ -493,7 +508,10 @@ def add_data_file( _logger.warning("[provenance] Unknown hash method %s for bagit manifest", Hasher) # Inefficient, bagit support need to checksum again self._add_to_bagit(rel_path) - _logger.debug("[provenance] Added data file %s", path) + if 'dir' in self.relativised_input_object: + _logger.debug("[provenance] Directory :%s", self.relativised_input_object['dir']['basename']) + else: + _logger.debug("[provenance] Added data file %s", path) if timestamp is not None: createdOn, createdBy = self._self_made(timestamp) self._file_provenance[rel_path] = cast( @@ -557,7 +575,10 @@ def _add_to_bagit(self, rel_path: str, **checksums: str) -> None: checksums = dict(checksums) with open(lpath, "rb") as file_path: # FIXME: Need sha-256 / sha-512 as well for Research Object BagIt profile? - checksums[SHA1] = checksum_copy(file_path, hasher=hashlib.sha1) + if self.no_data: + checksums[SHA1] = checksum_only(file_path, hasher=hashlib.sha1) + else: + checksums[SHA1] = checksum_copy(file_path, hasher=hashlib.sha1) self.add_to_manifest(rel_path, checksums) diff --git a/cwltool/executors.py b/cwltool/executors.py index 31c9b052c..6310c2005 100644 --- a/cwltool/executors.py +++ b/cwltool/executors.py @@ -172,7 +172,7 @@ def check_for_abstract_op(tool: CWLObjectType) -> None: ): process_run_id: Optional[str] = None name = "primary" - process.parent_wf.generate_output_prov(self.final_output[0], process_run_id, name) + process.parent_wf.generate_output_prov(self.final_output[0], process_run_id, name) # Note to self... # , "generate_output_prov") process.parent_wf.document.wasEndedBy( process.parent_wf.workflow_run_uri, None, diff --git a/cwltool/job.py b/cwltool/job.py index 2faf58779..a90b99e93 100644 --- a/cwltool/job.py +++ b/cwltool/job.py @@ -285,7 +285,7 @@ def _execute( and isinstance(job_order, (list, dict)) ): runtimeContext.prov_obj.used_artefacts( - job_order, runtimeContext.process_run_id, str(self.name) + job_order, runtimeContext.process_run_id, str(self.name), load_listing=self.builder.loadListing ) else: _logger.warning( @@ -411,6 +411,7 @@ def stderr_stdout_log_path( runtimeContext.process_run_id, outputs, datetime.datetime.now(), + # builder.loadListing # TODO FIX THIS ) if processStatus != "success": _logger.warning("[job %s] completed %s", self.name, processStatus) diff --git a/cwltool/main.py b/cwltool/main.py index 965f863a0..b670b3f36 100755 --- a/cwltool/main.py +++ b/cwltool/main.py @@ -11,6 +11,7 @@ import signal import subprocess # nosec import sys +import tempfile import time import urllib import warnings @@ -693,6 +694,7 @@ def setup_provenance( temp_prefix_ro=args.tmpdir_prefix, orcid=args.orcid, full_name=args.cwl_full_name, + no_data=args.no_data, ) runtimeContext.research_obj = ro log_file_io = open_log_file_for_activity(ro, ro.engine_uuid) @@ -1138,12 +1140,27 @@ def main( print(f"{args.workflow} is valid CWL.", file=stdout) return 0 - if args.print_rdf: + if args.print_rdf or args.provenance: + output = stdout + if args.provenance: + # Write workflow to temp directory + temp_workflow_dir = tempfile.TemporaryDirectory() + os.makedirs(temp_workflow_dir.name, exist_ok=True) + workflow_provenance = temp_workflow_dir.name + "/workflow.ttl" + # Sets up a turtle file for the workflow information (not yet in the provenance folder as it does + # not exist and creating it will give issues). + output = open(workflow_provenance, "w") + _logger.info("Writing workflow rdf to %s", workflow_provenance) print( printrdf(tool, loadingContext.loader.ctx, args.rdf_serializer), - file=stdout, + file=output, ) - return 0 + # close the output + if args.provenance: + output.close() + # Only print_rdf exits this way + if args.print_rdf: + return 0 if args.print_dot: printdot(tool, loadingContext.loader.ctx, stdout) diff --git a/tests/test_provenance.py b/tests/test_provenance.py index 83eb61c22..231da5afa 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -206,6 +206,8 @@ def test_directory_workflow(tmp_path: Path) -> None: p = folder / "data" / prefix / l_hash assert p.is_file(), f"Could not find {letter} as {p}" + # List content + list_files(tmp_path) @needs_docker def test_no_data_files(tmp_path: Path) -> None: @@ -787,3 +789,128 @@ def test_research_object() -> None: def test_research_object_picklability(research_object: ResearchObject) -> None: """Research object may need to be pickled (for Toil).""" assert pickle.dumps(research_object) is not None + + + +### Jasper + +import os + +def list_files(startpath): + startpath = str(startpath) + print("Root: ", startpath) + for root, dirs, files in os.walk(startpath): + level = root.replace(startpath, '').count(os.sep) + indent = ' ' * 4 * (level) + print('{}{}/'.format(indent, os.path.basename(root))) + subindent = ' ' * 4 * (level + 1) + for f in files: + print('{}{}'.format(subindent, f)) + + +@needs_docker +def test_directory_workflow_no_listing(tmp_path: Path) -> None: + """ + This test will check for 3 files that should be there and 3 files that should not be there. + @param tmp_path: + """ + + dir2 = tmp_path / "dir_deep_listing" + dir2.mkdir() + sha1 = { + # Expected hashes of ASCII letters (no linefeed) + # as returned from: + # for x in a b c ; do echo -n $x | sha1sum ; done + "a": "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8", + "b": "e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98", + "c": "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4", + } + for x in "abc": + # Make test files with predictable hashes + with open(dir2 / x, "w", encoding="ascii") as f: + f.write(x) + + dir3 = tmp_path / "dir_no_listing" + dir3.mkdir() + sha1 = { + # Expected hashes of ASCII letters (no linefeed) + # as returned from: + # for x in d e f ; do echo -n $x | sha1sum ; done + "d": "3c363836cf4e16666669a25da280a1865c2d2874", + "e": "58e6b3a414a1e090dfc6029add0f3555ccba127f", + "f": "4a0a19218e082a343a1b17e5333409af9d98f0f5", + } + for x in "def": + # Make test files with predictable hashes + with open(dir3 / x, "w", encoding="ascii") as f: + f.write(x) + + dir4 = tmp_path / "dir_no_info" + dir4.mkdir() + sha1 = { + # Expected hashes of ASCII letters (no linefeed) + # as returned from: + # for x in g h i ; do echo -n $x | sha1sum ; done + "g": "54fd1711209fb1c0781092374132c66e79e2241b", + "h": "27d5482eebd075de44389774fce28c69f45c8a75", + "i": "042dc4512fa3d391c5170cf3aa61e6a638f84342", + } + for x in "ghi": + # Make test files with predictable hashes + with open(dir4 / x, "w", encoding="ascii") as f: + f.write(x) + + folder = cwltool( + tmp_path, + get_data("tests/wf/directory_no_listing.cwl"), + "--dir", + str(dir2), + "--ignore", + str(dir3), + "--ignore_no_info", + str(dir4), + ) + + # Visualize the path structure + list_files(tmp_path) + + # check invert? as there should be no data in there + # check_provenance(folder, directory=True) + + # Output should include ls stdout of filenames a b c on each line + file_list = ( + folder + / "data" + / "84" + / "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4" + # checksum as returned from: + # echo -e "a\nb\nc" | sha1sum + # 3ca69e8d6c234a469d16ac28a4a658c92267c423 - + ) + # File should not exist... + assert not file_list.is_file() + + # Input files should be captured by hash value, + # even if they were inside a class: Directory + for (l, l_hash) in sha1.items(): + prefix = l_hash[:2] # first 2 letters + p = folder / "data" / prefix / l_hash + # File should be empty and in the future not existing... + # assert os.path.getsize(p.absolute()) == 0 + # To be discared when file really does not exist anymore + if l not in ['d', 'e', 'f', 'g', 'h', 'i']: + print("Analysing file %s", l) + assert p.is_file(), f"Could not find {l} as {p}" + +def cwltool_no_data(tmp_path: Path, *args: Any) -> Path: + prov_folder = tmp_path / "provenance" + prov_folder.mkdir() + new_args = ["--enable-ext", "--no-data", "--provenance", str(prov_folder)] + new_args.extend(args) + # Run within a temporary directory to not pollute git checkout + tmp_dir = tmp_path / "cwltool-run" + tmp_dir.mkdir() + with working_directory(tmp_dir): + status = main(new_args) + assert status == 0, f"Failed: cwltool.main({args})" + return prov_folder \ No newline at end of file diff --git a/tests/test_provenance.py::test_directory_workflow_no_listing b/tests/test_provenance.py::test_directory_workflow_no_listing new file mode 100644 index 000000000..06df4048d --- /dev/null +++ b/tests/test_provenance.py::test_directory_workflow_no_listing @@ -0,0 +1,32987 @@ +versions pytest-7.3.1, python-3.10.11.final.0 +cwd=/Users/jasperk/gitlab/cwltool +args=('--debug', 'tests/test_provenance.py::test_directory_workflow_no_listing', '--no-header', '--no-summary', '-q') + + pytest_plugin_registered [hook] + plugin: <__channelexec__.WorkerInteractor object at 0x1056a8d60> + manager: <_pytest.config.PytestPluginManager object at 0x104a400a0> + finish pytest_plugin_registered --> [] [hook] + pytest_cmdline_main [hook] + config: <_pytest.config.Config object at 0x105587730> + pytest_plugin_registered [hook] + plugin: + manager: 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pytest_plugin_registered [hook] + plugin: <_pytest.cacheprovider.NFPlugin object at 0x1056d4550> + manager: <_pytest.config.PytestPluginManager object at 0x104a400a0> + finish pytest_plugin_registered --> [] [hook] + pytest_plugin_registered [hook] + plugin: + manager: <_pytest.config.PytestPluginManager object at 0x104a400a0> + finish pytest_plugin_registered --> [] [hook] + pytest_plugin_registered [hook] + plugin: <_pytest.terminal.TerminalReporter object at 0x105f54910> + manager: <_pytest.config.PytestPluginManager object at 0x104a400a0> + finish pytest_plugin_registered --> [] [hook] + pytest_plugin_registered [hook] + plugin: <_pytest.logging.LoggingPlugin object at 0x105f56fb0> + manager: <_pytest.config.PytestPluginManager object at 0x104a400a0> + finish pytest_plugin_registered --> [] [hook] + pytest_plugin_registered [hook] + plugin: <_pytest.fixtures.FixtureManager object at 0x105fc81c0> + manager: <_pytest.config.PytestPluginManager object at 0x104a400a0> + finish pytest_plugin_registered --> [] [hook] + finish pytest_sessionstart --> [] [hook] + pytest_collection [hook] + session: testsfailed=0 testscollected=0> + perform_collect testsfailed=0 testscollected=0> ['tests'] [collection] + pytest_collectstart [hook] + collector: testsfailed=0 testscollected=0> + finish pytest_collectstart --> [] [hook] + pytest_make_collect_report [hook] + collector: testsfailed=0 testscollected=0> + processing argument (PosixPath('/Users/jasperk/gitlab/cwltool/tests'), []) [collection] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + finish pytest_ignore_collect --> None [hook] + pytest_collect_file [hook] + parent: testsfailed=0 testscollected=0> + file_path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + pytest_pycollect_makemodule [hook] + parent: testsfailed=0 testscollected=0> + module_path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + finish pytest_pycollect_makemodule --> [hook] + finish pytest_collect_file --> [] [hook] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + finish pytest_ignore_collect --> None [hook] + pytest_collect_file [hook] + parent: testsfailed=0 testscollected=0> + file_path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + pytest_pycollect_makemodule [hook] + parent: testsfailed=0 testscollected=0> + module_path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + path: /Users/jasperk/gitlab/cwltool/tests/__init__.py + finish pytest_pycollect_makemodule --> [hook] + finish pytest_collect_file --> [] [hook] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf + finish pytest_ignore_collect --> None [hook] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf.cwl + finish pytest_ignore_collect --> None [hook] + pytest_collect_file [hook] + parent: testsfailed=0 testscollected=0> + file_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf.cwl + finish pytest_collect_file --> [] [hook] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf2.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf2.cwl + finish pytest_ignore_collect --> None [hook] + pytest_collect_file [hook] + parent: testsfailed=0 testscollected=0> + file_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf2.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf2.cwl + finish pytest_collect_file --> [] [hook] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf3.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf3.cwl + finish pytest_ignore_collect --> None [hook] + pytest_collect_file [hook] + parent: testsfailed=0 testscollected=0> + file_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf3.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf3.cwl + finish pytest_collect_file --> [] [hook] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf4.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf4.cwl + finish pytest_ignore_collect --> None [hook] + pytest_collect_file [hook] + parent: testsfailed=0 testscollected=0> + file_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf4.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/broken-wf4.cwl + finish pytest_collect_file --> [] [hook] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/cat-a.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/cat-a.cwl + finish pytest_ignore_collect --> None [hook] + pytest_collect_file [hook] + parent: testsfailed=0 testscollected=0> + file_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/cat-a.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/cat-a.cwl + finish pytest_collect_file --> [] [hook] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/cat.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/cat.cwl + finish pytest_ignore_collect --> None [hook] + pytest_collect_file [hook] + parent: testsfailed=0 testscollected=0> + file_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/cat.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/cat.cwl + finish pytest_collect_file --> [] [hook] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/circ-dep-wf.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/circ-dep-wf.cwl + finish pytest_ignore_collect --> None [hook] + pytest_collect_file [hook] + parent: testsfailed=0 testscollected=0> + file_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/circ-dep-wf.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/circ-dep-wf.cwl + finish pytest_collect_file --> [] [hook] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/circ-dep-wf2.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/circ-dep-wf2.cwl + finish pytest_ignore_collect --> None [hook] + pytest_collect_file [hook] + parent: testsfailed=0 testscollected=0> + file_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/circ-dep-wf2.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/circ-dep-wf2.cwl + finish pytest_collect_file --> [] [hook] + pytest_ignore_collect [hook] + config: <_pytest.config.Config object at 0x105587730> + collection_path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/echo.cwl + path: /Users/jasperk/gitlab/cwltool/tests/checker_wf/echo.cwl + finish pytest_ignore_collect --> None [hook] + pytest_collect_file [hook] + parent: testsfailed=0 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[assertion] + finish pytest_xdist_newgateway --> [] [hook] + pytest_plugin_registered [hook] + plugin: + manager: <_pytest.config.PytestPluginManager object at 0x1107c4070> + finish pytest_plugin_registered --> [] [hook] + pytest_configure_node [hook] + node: + finish pytest_configure_node --> [] [hook] + pytest_xdist_getremotemodule [hook] + finish pytest_xdist_getremotemodule --> [hook] + started node [config:nodemanager] + pytest_xdist_newgateway [hook] + gateway: + early skip of rewriting module: __builtin__ [assertion] + finish pytest_xdist_newgateway --> [] [hook] + pytest_plugin_registered [hook] + plugin: + manager: <_pytest.config.PytestPluginManager object at 0x1107c4070> + finish pytest_plugin_registered --> [] [hook] + pytest_configure_node [hook] + node: + finish pytest_configure_node --> [] [hook] + pytest_xdist_getremotemodule [hook] + finish pytest_xdist_getremotemodule --> [hook] + started node [config:nodemanager] + pytest_xdist_newgateway [hook] + gateway: + early 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nodeid: + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : PytestCollectionWarning("cannot collect test class 'TestFsAccess' because it has a __init__ constructor (from: tests/test_path_checks.py)"), category : 'PytestCollectionWarning', filename : '/Users/jasperk/gitlab/cwltool/tests/test_path_checks.py', lineno : 110, line : None} + when: collect + nodeid: + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_xdist_node_collection_finished [hook] + node: + ids: ['tests/test_anon_types.py::test_anon_types[snippet0]', 'tests/test_anon_types.py::test_anon_types[snippet1]', 'tests/test_check.py::test_output_checking[tests/wf/badout1.cwl]', 'tests/test_check.py::test_output_checking[tests/wf/badout2.cwl]', 'tests/test_check.py::test_output_checking[tests/wf/badout3.cwl]', 'tests/test_conditionals.py::test_conditional_step_no_inputs', 'tests/test_content_type.py::test_content_types', 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nodeid: + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : PytestCollectionWarning("cannot collect test class 'TestFsAccess' because it has a __init__ constructor (from: tests/test_path_checks.py)"), category : 'PytestCollectionWarning', filename : '/Users/jasperk/gitlab/cwltool/tests/test_path_checks.py', lineno : 110, line : None} + when: collect + nodeid: + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_xdist_node_collection_finished [hook] + node: + ids: ['tests/test_anon_types.py::test_anon_types[snippet0]', 'tests/test_anon_types.py::test_anon_types[snippet1]', 'tests/test_check.py::test_output_checking[tests/wf/badout1.cwl]', 'tests/test_check.py::test_output_checking[tests/wf/badout2.cwl]', 'tests/test_check.py::test_output_checking[tests/wf/badout3.cwl]', 'tests/test_conditionals.py::test_conditional_step_no_inputs', 'tests/test_content_type.py::test_content_types', 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nodeid: + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : PytestCollectionWarning("cannot collect test class 'TestFsAccess' because it has a __init__ constructor (from: tests/test_path_checks.py)"), category : 'PytestCollectionWarning', filename : '/Users/jasperk/gitlab/cwltool/tests/test_path_checks.py', lineno : 110, line : None} + when: collect + nodeid: + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_xdist_node_collection_finished [hook] + node: + ids: ['tests/test_anon_types.py::test_anon_types[snippet0]', 'tests/test_anon_types.py::test_anon_types[snippet1]', 'tests/test_check.py::test_output_checking[tests/wf/badout1.cwl]', 'tests/test_check.py::test_output_checking[tests/wf/badout2.cwl]', 'tests/test_check.py::test_output_checking[tests/wf/badout3.cwl]', 'tests/test_conditionals.py::test_conditional_step_no_inputs', 'tests/test_content_type.py::test_content_types', 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nodeid: + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : PytestCollectionWarning("cannot collect test class 'TestFsAccess' because it has a __init__ constructor (from: tests/test_path_checks.py)"), category : 'PytestCollectionWarning', filename : '/Users/jasperk/gitlab/cwltool/tests/test_path_checks.py', lineno : 110, line : None} + when: collect + nodeid: + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_xdist_node_collection_finished [hook] + node: + ids: ['tests/test_anon_types.py::test_anon_types[snippet0]', 'tests/test_anon_types.py::test_anon_types[snippet1]', 'tests/test_check.py::test_output_checking[tests/wf/badout1.cwl]', 'tests/test_check.py::test_output_checking[tests/wf/badout2.cwl]', 'tests/test_check.py::test_output_checking[tests/wf/badout3.cwl]', 'tests/test_conditionals.py::test_conditional_step_no_inputs', 'tests/test_content_type.py::test_content_types', 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'tests/test_validate.py::test_validate_graph_with_no_default', 'tests/test_validate_js.py::test_get_expressions', 'tests/test_validate_js.py::test_validate_js_expressions', 'tests/test_validate_js.py::test_js_hint_basic', 'tests/test_validate_js.py::test_js_hint_reports_invalid_js', 'tests/test_validate_js.py::test_js_hint_warn_on_es6', 'tests/test_validate_js.py::test_js_hint_error_on_undefined_name', 'tests/test_validate_js.py::test_js_hint_set_defined_name', 'tests/test_windows_warning.py::test_windows_warning'] + finish pytest_xdist_node_collection_finished --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : DeprecationWarning("the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses"), category : 'DeprecationWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/util/path/__init__.py', lineno : 5, line : None} + when: collect + nodeid: + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : PytestCollectionWarning("cannot collect test class 'TestFsAccess' because it has a __init__ constructor (from: tests/test_path_checks.py)"), category : 'PytestCollectionWarning', filename : '/Users/jasperk/gitlab/cwltool/tests/test_path_checks.py', lineno : 110, line : None} + when: collect + nodeid: + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_anon_types.py::test_anon_types[snippet0] + location: ('tests/test_anon_types.py', 116, 'test_anon_types[snippet0]') + early skip of rewriting module: _jb_parallel_tree_manager [assertion] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_cuda.py::test_cuda_eval_resource_max', 'location': ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max'), 'keywords': 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'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005695310001101461, 'start': 1685951407.1618838, 'stop': 1685951407.162456, '$report_type': 'TestReport', 'item_index': 81, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo ["bar"])-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo ["bar"])-False]'), 'keywords': {'test_expression_match[(foo ["bar"])-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo ["bar"])-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007806869998603361, 'start': 1685951407.164284, 'stop': 1685951407.165066, '$report_type': 'TestReport', 'item_index': 62, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz'])-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz'])-zab1]"), 'keywords': {"test_expression_interpolate[$(foo.bar['baz'])-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['baz'])-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004662589999497868, 'start': 1685951407.1631842, 'stop': 1685951407.163651, '$report_type': 'TestReport', 'item_index': 81, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +Õرnify Úر1th)HÕرondit Úر pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0007384439995803405, 'start': 1685951407.1622689, 'stop': 1685951407.163012, '$report_type': 'TestReport', 'item_index': 101, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004903330000161077, 'start': 1685951407.1636748, 'stop': 1685951407.164167, '$report_type': 'TestReport', 'item_index': 101, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_cuda.py::test_cuda_eval_resource_max + location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]"), 'keywords': {"test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].baz)-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006115910000517033, 'start': 1685951407.164877, 'stop': 1685951407.16549, '$report_type': 'TestReport', 'item_index': 82, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]"), 'keywords': {"test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].baz)-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003998640004283516, 'start': 1685951407.166046, 'stop': 1685951407.166448, '$report_type': 'TestReport', 'item_index': 82, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo ["bar"])-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo ["bar"])-False]'), 'keywords': {'test_expression_match[(foo ["bar"])-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo ["bar"])-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003943009996874025, 'start': 1685951407.16566, 'stop': 1685951407.166056, '$report_type': 'TestReport', 'item_index': 62, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_empty_input.py::test_empty_input + location: ('tests/test_empty_input.py', 8, 'test_empty_input') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo ["bar"])-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo ["bar"])-False]'), 'keywords': {'test_expression_match[(foo ["bar"])-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo ["bar"])-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00045918899922980927, 'start': 1685951407.1667142, 'stop': 1685951407.1671748, '$report_type': 'TestReport', 'item_index': 62, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar']["baz"])-zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']["baz"])-zab1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005238170006123255, 'start': 1685951407.165504, 'stop': 1685951407.166029, '$report_type': 'TestReport', 'item_index': 102, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[( foo["bar"])-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[( foo["bar"])-False]'), 'keywords': {'test_expression_match[( foo["bar"])-False]': 1, 'parametrize': 1, 'pytestmark': 1, '( foo["bar"])-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006716450006933883, 'start': 1685951407.168631, 'stop': 1685951407.1693041, '$report_type': 'TestReport', 'item_index': 63, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00046043899965297896, 'start': 1685951407.1664672, 'stop': 1685951407.166929, '$report_type': 'TestReport', 'item_index': 102, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar) $(foo.bar)-{"baz": "zab1"} {"baz": "zab1"}] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar) $(foo.bar)-{"baz": "zab1"} {"baz": "zab1"}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["b\'ar"].baz)-True]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\'ar"].baz)-True]'), 'keywords': {'test_expression_interpolate[$(foo["b\'ar"].baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\'ar"].baz)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006500110002889414, 'start': 1685951407.168532, 'stop': 1685951407.169183, '$report_type': 'TestReport', 'item_index': 83, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[( foo["bar"])-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[( foo["bar"])-False]'), 'keywords': {'test_expression_match[( foo["bar"])-False]': 1, 'parametrize': 1, 'pytestmark': 1, '( foo["bar"])-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005849190001754323, 'start': 1685951407.169935, 'stop': 1685951407.170521, '$report_type': 'TestReport', 'item_index': 63, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004279869999663788, 'start': 1685951407.167524, 'stop': 1685951407.167954, '$report_type': 'TestReport', 'item_index': 102, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + "tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]", 'tests/test_examples.py::test_expression_interpolate[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]', "tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]", "tests/test_examples.py::test_expression_interpolate[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]", "tests/test_examples.py::test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]", 'tests/test_examples.py::test_expression_interpolate[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]', 'tests/test_examples.py::test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]', 'tests/test_examples.py::test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]', 'tests/test_examples.py::test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]', 'tests/test_examples.py::test_parameter_ finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["b\'ar"].baz)-True]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\'ar"].baz)-True]'), 'keywords': {'test_expression_interpolate[$(foo["b\'ar"].baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\'ar"].baz)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00042951199975505006, 'start': 1685951407.169718, 'stop': 1685951407.170149, '$report_type': 'TestReport', 'item_index': 83, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["b\'ar"].baz)-True]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\'ar"].baz)-True]'), 'keywords': {'test_expression_interpolate[$(foo["b\'ar"].baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\'ar"].baz)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00040715600061957957, 'start': 1685951407.1707578, 'stop': 1685951407.171166, '$report_type': 'TestReport', 'item_index': 83, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[( foo["bar"])-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[( foo["bar"])-False]'), 'keywords': {'test_expression_match[( foo["bar"])-False]': 1, 'parametrize': 1, 'pytestmark': 1, '( foo["bar"])-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003380090001883218, 'start': 1685951407.171147, 'stop': 1685951407.171486, '$report_type': 'TestReport', 'item_index': 63, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]'), 'keywords': {'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006886129995109513, 'start': 1685951407.169198, 'stop': 1685951407.169888, '$report_type': 'TestReport', 'item_index': 103, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]'), 'keywords': {'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005928349992245785, 'start': 1685951407.1704981, 'stop': 1685951407.171092, '$report_type': 'TestReport', 'item_index': 103, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]'), 'keywords': {'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz)-None': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008802599995760829, 'start': 1685951407.172412, 'stop': 1685951407.173294, '$report_type': 'TestReport', 'item_index': 84, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +ÐV@V°V V V!VPúTp!V°úTûTpûTÐûT0üTà!V0qF°èU0éU°éU0êUP"VüTÀ"V0#VðüTPýT #V°ýTþT$VpþTÐþT€$V0ÿTð$V`%VÐ%V@&VÿT°êU0ëU0@V°&V 'V'V(Vp(Và(V pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]'), 'keywords': {'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003808780002145795, 'start': 1685951407.1716611, 'stop': 1685951407.172043, '$report_type': 'TestReport', 'item_index': 103, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo[bar].baz)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo[bar].baz)-False]'), 'keywords': {'test_expression_match[(foo[bar].baz)-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo[bar].baz)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009385580005982774, 'start': 1685951407.1726239, 'stop': 1685951407.173565, '$report_type': 'TestReport', 'item_index': 64, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo[bar].baz)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo[bar].baz)-False]'), 'keywords': {'test_expression_match[(foo[bar].baz)-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo[bar].baz)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000691512000230432, 'start': 1685951407.174499, 'stop': 1685951407.175193, '$report_type': 'TestReport', 'item_index': 64, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]'), 'keywords': {'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz)-None': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003795280008489499, 'start': 1685951407.175756, 'stop': 1685951407.176137, '$report_type': 'TestReport', 'item_index': 84, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo['b\\'ar'].baz)--true] + location: ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['b\\\\'ar'].baz)--true]") + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo[bar].baz)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo[bar].baz)-False]'), 'keywords': {'test_expression_match[(foo[bar].baz)-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo[bar].baz)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00034629699985089246, 'start': 1685951407.1757581, 'stop': 1685951407.176105, '$report_type': 'TestReport', 'item_index': 64, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] +ession_interpolate[-$(foo['b\\\\'ar'].baz)--true]", 'tests/test_examples.py::test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]', 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]', 'tests/test_examples.py::test_expression_interpolate[$(foo.bar) $(foo.bar)-{"baz": "zab1"} {"baz": "zab1"}]', 'tests/test_examples.py::test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]', 'tests/test_examples.py::test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]', 'tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]', "tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]", 'tests/test_examples.py::test_expression_interpolate[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]', "tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]", "tests/test_examples.py::test_expression_interpol pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]"), 'keywords': {"test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001335947000370652, 'start': 1685951407.1736891, 'stop': 1685951407.175027, '$report_type': 'TestReport', 'item_index': 104, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]"), 'keywords': {"test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005527040002561989, 'start': 1685951407.175524, 'stop': 1685951407.176078, '$report_type': 'TestReport', 'item_index': 104, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\x-x-1] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(lst[0])-A]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst[0])-A]'), 'keywords': {'test_expression_interpolate[$(lst[0])-A]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[0])-A': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006926320002094144, 'start': 1685951407.177449, 'stop': 1685951407.178143, '$report_type': 'TestReport', 'item_index': 85, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(lst[0])-A]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst[0])-A]'), 'keywords': {'test_expression_interpolate[$(lst[0])-A]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[0])-A': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004155910000918084, 'start': 1685951407.178727, 'stop': 1685951407.179144, '$report_type': 'TestReport', 'item_index': 85, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]"), 'keywords': {"test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00042704199950094335, 'start': 1685951407.176735, 'stop': 1685951407.1771631, '$report_type': 'TestReport', 'item_index': 104, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(lst[0])-A]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst[0])-A]'), 'keywords': {'test_expression_interpolate[$(lst[0])-A]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[0])-A': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003655159998743329, 'start': 1685951407.1796749, 'stop': 1685951407.180042, '$report_type': 'TestReport', 'item_index': 85, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo[\'bar"].baz)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo[\'bar"].baz)-False]'), 'keywords': {'test_expression_match[(foo[\'bar"].baz)-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo[\'bar"].baz)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00067913899965788, 'start': 1685951407.177366, 'stop': 1685951407.178047, '$report_type': 'TestReport', 'item_index': 65, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo[\'bar"].baz)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo[\'bar"].baz)-False]'), 'keywords': {'test_expression_match[(foo[\'bar"].baz)-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo[\'bar"].baz)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003521799999361974, 'start': 1685951407.178601, 'stop': 1685951407.178955, '$report_type': 'TestReport', 'item_index': 65, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo[\'bar"].baz)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo[\'bar"].baz)-False]'), 'keywords': {'test_expression_match[(foo[\'bar"].baz)-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo[\'bar"].baz)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003992160000052536, 'start': 1685951407.1794848, 'stop': 1685951407.179886, '$report_type': 'TestReport', 'item_index': 65, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(lst[1])-B]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst[1])-B]'), 'keywords': {'test_expression_interpolate[$(lst[1])-B]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[1])-B': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005827159993714304, 'start': 1685951407.181282, 'stop': 1685951407.181866, '$report_type': 'TestReport', 'item_index': 86, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(lst[1])-B]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst[1])-B]'), 'keywords': {'test_expression_interpolate[$(lst[1])-B]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[1])-B': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003729469999598223, 'start': 1685951407.1824079, 'stop': 1685951407.182783, '$report_type': 'TestReport', 'item_index': 86, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]'), 'keywords': {'test_expression_interpolate[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006820569997216808, 'start': 1685951407.178524, 'stop': 1685951407.179208, '$report_type': 'TestReport', 'item_index': 105, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] +olate[$(foo['bar'].baz) $(foo['bar'].baz)-z°äKexamples.py::test_expression_interpolate[$(foo[\'bar\'][°ªbaz"])-zab1 zab1]', "tests/test_examples.py::test_expresÀãKar['baz']) $(foo.bar['baz'])-zab1 zab1]", "tests/test_ex`¬on_interpolate[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2°ª.py::test_expression_interpolate[$(foo['b\\\\'ar'].baz) PäKrue true]", 'tests/test pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(lst[1])-B]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst[1])-B]'), 'keywords': {'test_expression_interpolate[$(lst[1])-B]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[1])-B': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00035604000004241243, 'start': 1685951407.183312, 'stop': 1685951407.183669, '$report_type': 'TestReport', 'item_index': 86, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_match[(foo['bar].baz)-False]", 'location': ('tests/test_examples.py', 64, "test_expression_match[(foo['bar].baz)-False]"), 'keywords': {"test_expression_match[(foo['bar].baz)-False]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar].baz)-False": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005624340001304518, 'start': 1685951407.181042, 'stop': 1685951407.1816058, '$report_type': 'TestReport', 'item_index': 66, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]'), 'keywords': {'test_expression_interpolate[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00044064299981982913, 'start': 1685951407.180925, 'stop': 1685951407.1813672, '$report_type': 'TestReport', 'item_index': 105, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar) $(foo.bar)-{"baz": "zab1"} {"baz": "zab1"}] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar) $(foo.bar)-{"baz": "zab1"} {"baz": "zab1"}]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(lst.length)-2]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst.length)-2]'), 'keywords': {'test_expression_interpolate[$(lst.length)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst.length)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005320390000633779, 'start': 1685951407.184791, 'stop': 1685951407.185324, '$report_type': 'TestReport', 'item_index': 87, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_match[(foo['bar].baz)-False]", 'location': ('tests/test_examples.py', 64, "test_expression_match[(foo['bar].baz)-False]"), 'keywords': {"test_expression_match[(foo['bar].baz)-False]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar].baz)-False": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002296920001754188, 'start': 1685951407.18209, 'stop': 1685951407.1823208, '$report_type': 'TestReport', 'item_index': 66, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(lst.length)-2]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst.length)-2]'), 'keywords': {'test_expression_interpolate[$(lst.length)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst.length)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003584709993447177, 'start': 1685951407.185848, 'stop': 1685951407.186207, '$report_type': 'TestReport', 'item_index': 87, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] +olate[$(foo['bar'].baz) $(foo['bar'].baz)-z°äKexamples.py::test_expression_interpolate[$(foo[\'bar\'][°ªbaz"])-zab1 zab1]', "tests/test_examples.py::test_expresÀãKar['baz']) $(foo.bar['baz'])-zab1 zab1]", "tests/test_ex`¬on_interpolate[$(foo['b ar'].baz) $(f pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_match[(foo['bar].baz)-False]", 'location': ('tests/test_examples.py', 64, "test_expression_match[(foo['bar].baz)-False]"), 'keywords': {"test_expression_match[(foo['bar].baz)-False]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar].baz)-False": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00033253899982810253, 'start': 1685951407.182771, 'stop': 1685951407.183105, '$report_type': 'TestReport', 'item_index': 66, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(lst.length)-2]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst.length)-2]'), 'keywords': {'test_expression_interpolate[$(lst.length)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst.length)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003409870005270932, 'start': 1685951407.186731, 'stop': 1685951407.187073, '$report_type': 'TestReport', 'item_index': 87, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]"), 'keywords': {"test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005447009998533758, 'start': 1685951407.182559, 'stop': 1685951407.183105, '$report_type': 'TestReport', 'item_index': 106, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[{foo}-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[{foo}-False]'), 'keywords': {'test_expression_match[{foo}-False]': 1, 'parametrize': 1, 'pytestmark': 1, '{foo}-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005385439999372466, 'start': 1685951407.184143, 'stop': 1685951407.184683, '$report_type': 'TestReport', 'item_index': 67, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.["bar"])-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.["bar"])-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]"), 'keywords': {"test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005313980000209995, 'start': 1685951407.183653, 'stop': 1685951407.184185, '$report_type': 'TestReport', 'item_index': 106, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(lst['length'])-2]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(lst['length'])-2]"), 'keywords': {"test_expression_interpolate[$(lst['length'])-2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(lst['length'])-2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000505391000842792, 'start': 1685951407.188127, 'stop': 1685951407.1886332, '$report_type': 'TestReport', 'item_index': 88, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[{foo}-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[{foo}-False]'), 'keywords': {'test_expression_match[{foo}-False]': 1, 'parametrize': 1, 'pytestmark': 1, '{foo}-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002932269999291748, 'start': 1685951407.185169, 'stop': 1685951407.1854641, '$report_type': 'TestReport', 'item_index': 67, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[{foo}-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[{foo}-False]'), 'keywords': {'test_expression_match[{foo}-False]': 1, 'parametrize': 1, 'pytestmark': 1, '{foo}-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00036646900025516516, 'start': 1685951407.185961, 'stop': 1685951407.1863291, '$report_type': 'TestReport', 'item_index': 67, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(lst['length'])-2]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(lst['length'])-2]"), 'keywords': {"test_expression_interpolate[$(lst['length'])-2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(lst['length'])-2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00032855400058906525, 'start': 1685951407.189135, 'stop': 1685951407.189465, '$report_type': 'TestReport', 'item_index': 88, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(lst['length'])-2]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(lst['length'])-2]"), 'keywords': {"test_expression_interpolate[$(lst['length'])-2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(lst['length'])-2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00039985099920158973, 'start': 1685951407.18994, 'stop': 1685951407.1903412, '$report_type': 'TestReport', 'item_index': 88, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo.bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar-False]'), 'keywords': {'test_expression_match[(foo.bar-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005366319992390345, 'start': 1685951407.1874418, 'stop': 1685951407.18798, '$report_type': 'TestReport', 'item_index': 68, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar']["baz"])-zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']["baz"])-zab1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo.bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar-False]'), 'keywords': {'test_expression_match[(foo.bar-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002336329998797737, 'start': 1685951407.1883898, 'stop': 1685951407.1886249, '$report_type': 'TestReport', 'item_index': 68, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo.bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar-False]'), 'keywords': {'test_expression_match[(foo.bar-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002501280005162698, 'start': 1685951407.18901, 'stop': 1685951407.189261, '$report_type': 'TestReport', 'item_index': 68, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.bar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.bar)-False]'), 'keywords': {'test_expression_match[foo.bar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008627580000393209, 'start': 1685951407.1903841, 'stop': 1685951407.191249, '$report_type': 'TestReport', 'item_index': 69, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.bar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.bar)-False]'), 'keywords': {'test_expression_match[foo.bar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004924349996144883, 'start': 1685951407.192138, 'stop': 1685951407.192632, '$report_type': 'TestReport', 'item_index': 69, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.bar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.bar)-False]'), 'keywords': {'test_expression_match[foo.bar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003537920001690509, 'start': 1685951407.1931489, 'stop': 1685951407.193504, '$report_type': 'TestReport', 'item_index': 69, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.b ar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.b ar)-False]'), 'keywords': {'test_expression_match[foo.b ar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.b ar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005005540006095544, 'start': 1685951407.194539, 'stop': 1685951407.195041, '$report_type': 'TestReport', 'item_index': 70, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.b ar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.b ar)-False]'), 'keywords': {'test_expression_match[foo.b ar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.b ar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003098170000157552, 'start': 1685951407.195513, 'stop': 1685951407.1958241, '$report_type': 'TestReport', 'item_index': 70, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz'])-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz'])-zab1]"), 'keywords': {"test_expression_interpolate[$(foo.bar['baz'])-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['baz'])-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005695310001101461, 'start': 1685951407.1618838, 'stop': 1685951407.162456, '$report_type': 'TestReport', 'item_index': 81, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo ["bar"])-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo ["bar"])-False]'), 'keywords': {'test_expression_match[(foo ["bar"])-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo ["bar"])-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007806869998603361, 'start': 1685951407.164284, 'stop': 1685951407.165066, '$report_type': 'TestReport', 'item_index': 62, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz'])-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz'])-zab1]"), 'keywords': {"test_expression_interpolate[$(foo.bar['baz'])-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['baz'])-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004662589999497868, 'start': 1685951407.1631842, 'stop': 1685951407.163651, '$report_type': 'TestReport', 'item_index': 81, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +Õرnify Úر1th)HÕرondit Úر1PrechÕرshead Úر1)iˆÕر EntpÞUezEntity is + +equeÚongzÚ +uppoÈÕرpNTity + +jform0equekot S0CannXÖرleque0zxÖرm Fai0cond˜Öرnnot 0)i¢¸Öرoeapo0fuseØÖرsffee0is aø pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar']) $(foo['bar'])-{"baz": "zab1"} {"baz": "zab1"}] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]') + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.b ar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.b ar)-False]'), 'keywords': {'test_expression_match[foo.b ar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.b ar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003831390004052082, 'start': 1685951407.196325, 'stop': 1685951407.1967092, '$report_type': 'TestReport', 'item_index': 70, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar)--{"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007611769997311058, 'start': 1685951407.192053, 'stop': 1685951407.192816, '$report_type': 'TestReport', 'item_index': 89, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar)--{"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005116140000609448, 'start': 1685951407.193291, 'stop': 1685951407.193804, '$report_type': 'TestReport', 'item_index': 89, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar)--{"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003423060006753076, 'start': 1685951407.1943529, 'stop': 1685951407.194697, '$report_type': 'TestReport', 'item_index': 89, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\'])--{"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005454469992400846, 'start': 1685951407.195773, 'stop': 1685951407.19632, '$report_type': 'TestReport', 'item_index': 90, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_match[foo.b'ar)-False]", 'location': ('tests/test_examples.py', 64, "test_expression_match[foo.b'ar)-False]"), 'keywords': {"test_expression_match[foo.b'ar)-False]": 1, 'parametrize': 1, 'pytestmark': 1, "foo.b'ar)-False": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005132740006956737, 'start': 1685951407.197866, 'stop': 1685951407.198381, '$report_type': 'TestReport', 'item_index': 71, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]"), 'keywords': {"test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004594960000758874, 'start': 1685951407.18926, 'stop': 1685951407.1897202, '$report_type': 'TestReport', 'item_index': 108, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\'])--{"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00037809100012964336, 'start': 1685951407.196776, 'stop': 1685951407.197155, '$report_type': 'TestReport', 'item_index': 90, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_match[foo.b'ar)-False]", 'location': ('tests/test_examples.py', 64, "test_expression_match[foo.b'ar)-False]"), 'keywords': {"test_expression_match[foo.b'ar)-False]": 1, 'parametrize': 1, 'pytestmark': 1, "foo.b'ar)-False": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00021926200042798882, 'start': 1685951407.198775, 'stop': 1685951407.198996, '$report_type': 'TestReport', 'item_index': 71, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\'])--{"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00033905500004038913, 'start': 1685951407.197654, 'stop': 1685951407.197995, '$report_type': 'TestReport', 'item_index': 90, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]"), 'keywords': {"test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006865939994895598, 'start': 1685951407.1901271, 'stop': 1685951407.190815, '$report_type': 'TestReport', 'item_index': 108, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]"), 'keywords': {"test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007353870005317731, 'start': 1685951407.191674, 'stop': 1685951407.192411, '$report_type': 'TestReport', 'item_index': 108, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_match[foo.b'ar)-False]", 'location': ('tests/test_examples.py', 64, "test_expression_match[foo.b'ar)-False]"), 'keywords': {"test_expression_match[foo.b'ar)-False]": 1, 'parametrize': 1, 'pytestmark': 1, "foo.b'ar)-False": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00035343100080353906, 'start': 1685951407.1993961, 'stop': 1685951407.199751, '$report_type': 'TestReport', 'item_index': 71, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["bar"])--{"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005321990001903032, 'start': 1685951407.1991239, 'stop': 1685951407.199657, '$report_type': 'TestReport', 'item_index': 91, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["bar"])--{"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00033932099995581666, 'start': 1685951407.200981, 'stop': 1685951407.201321, '$report_type': 'TestReport', 'item_index': 91, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo+bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo+bar-False]'), 'keywords': {'test_expression_match[(foo+bar-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo+bar-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003839760001937975, 'start': 1685951407.200552, 'stop': 1685951407.200937, '$report_type': 'TestReport', 'item_index': 72, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo+bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo+bar-False]'), 'keywords': {'test_expression_match[(foo+bar-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo+bar-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00022087999968789518, 'start': 1685951407.201235, 'stop': 1685951407.2014568, '$report_type': 'TestReport', 'item_index': 72, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo.bar.baz)--zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar.baz)--zab1]'), 'keywords': {'test_expression_interpolate[-$(foo.bar.baz)--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.baz)--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005919989998801611, 'start': 1685951407.202494, 'stop': 1685951407.203087, '$report_type': 'TestReport', 'item_index': 92, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo+bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo+bar-False]'), 'keywords': {'test_expression_match[(foo+bar-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo+bar-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00041151400000671856, 'start': 1685951407.2019148, 'stop': 1685951407.202328, '$report_type': 'TestReport', 'item_index': 72, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz'])-zab1] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz'])-zab1]") + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo.bar.baz)--zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar.baz)--zab1]'), 'keywords': {'test_expression_interpolate[-$(foo.bar.baz)--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.baz)--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003540979996614624, 'start': 1685951407.203454, 'stop': 1685951407.203809, '$report_type': 'TestReport', 'item_index': 92, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +£¦»€¸œ„ÆðG£€(§Ýy‹ƒ½Ò0H£Ð(§^Ž¸.Ñ.õpH£P¦wU9ìKÓ~°H£@¦×HnÏ.€cÐðH£€¦(éÚ®_ìnÄ0I£ )§ÅâÖñ$ŒpI£p)§ù~ 6X*ºm°I£À)§àøhF÷2cðI£*§p¥‘½ÒÆÓ§0J£`*§\·Ñ¤s‹pîpJ£°*§E·ó@†°J£+§L/Ð-¥ïfðJ£À¸¦‚y¶s¼òRÍ0K£P+§.Øi|°*ÖpK£ +§m=Ô˜bìp›°K£p§Xˆ+`E…ðK£ð§ªÁvȹÔ0L£À§‚¿'ÑþØ>pL£ð+§à´9ßõÜŒ¨°L£p§±ºÂòyi¸@ðL£@,§Ø\¼ÍnŽC0M£ §+Æã uÄëpM£,§ŸoxÏì`s°M£à,§@CEÇß6ðM£à硈'®¨<Ñ +0N£ê¡†7ÅâÕÕpN£`ꡈ.£HÑyö¥°N£ ë¡Ý[}¼êá'ðN£ì¡Æ)váâÒ0O£0-§Ç%v”?ðï΀-§ìÑ0ÿÃFšpO£pÄmzúB¬‘°veÐ-§œ±]z¾°O£ .§‡¶Q5O)¤ðO£ ø¡v$ TÞݱ0P£p.§]#~KÐpP£`ù¡PÅEÇŽˆ@@°P£ú¡ÃX¥ÉP5ðP£À.§Õb—ÿ®l0ðÎ/§cqC…!ý 0Q£pÚ£±ãŒkäùpQ£`/§kÝ~bŽ÷y°Q£°/§VcUƒcp½ pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo.bar.baz)--zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar.baz)--zab1]'), 'keywords': {'test_expression_interpolate[-$(foo.bar.baz)--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.baz)--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002487620004103519, 'start': 1685951407.20425, 'stop': 1685951407.2045, '$report_type': 'TestReport', 'item_index': 92, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo bar-False]'), 'keywords': {'test_expression_match[(foo bar-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo bar-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000565628000003926, 'start': 1685951407.203383, 'stop': 1685951407.2039502, '$report_type': 'TestReport', 'item_index': 73, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]'), 'keywords': {'test_expression_interpolate[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005376529998102342, 'start': 1685951407.194816, 'stop': 1685951407.195355, '$report_type': 'TestReport', 'item_index': 109, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]'), 'keywords': {'test_expression_interpolate[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000326848999975482, 'start': 1685951407.195848, 'stop': 1685951407.1961758, '$report_type': 'TestReport', 'item_index': 109, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo bar-False]'), 'keywords': {'test_expression_match[(foo bar-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo bar-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002997560004587285, 'start': 1685951407.204415, 'stop': 1685951407.204716, '$report_type': 'TestReport', 'item_index': 73, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]'), 'keywords': {'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000499596999361529, 'start': 1685951407.197353, 'stop': 1685951407.197854, '$report_type': 'TestReport', 'item_index': 110, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz'])-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz'])-zab1]"), 'keywords': {"test_expression_interpolate[$(foo.bar['baz'])-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['baz'])-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004662589999497868, 'start': 1685951407.1631842, 'stop': 1685951407.163651, '$report_type': 'TestReport', 'item_index': 81, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +Õرnify Úر1th)HÕرondit Úر1PrechÕرshead Úر1)iˆÕر EntpÞUezEntity is + +equeÚongzÚ +uppoÈÕرpNTity + +jform0equekot S0CannXÖرleque0zxÖرm Fai0cond˜Öرnnot 0)i¢¸Öرoeapo0fuseØÖرsffee0is aøرrz0 Req×رp is 0prod8×ر]se)0cessX×ر\i§0i¨x×ر[pend pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo bar-False]'), 'keywords': {'test_expression_match[(foo bar-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo bar-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00036665500010713004, 'start': 1685951407.205195, 'stop': 1685951407.205562, '$report_type': 'TestReport', 'item_index': 73, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]'), 'keywords': {'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004955550002705422, 'start': 1685951407.1983428, 'stop': 1685951407.1988401, '$report_type': 'TestReport', 'item_index': 110, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo['bar'].baz)--zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['bar'].baz)--zab1]"), 'keywords': {"test_expression_interpolate[-$(foo['bar'].baz)--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].baz)--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006265920001169434, 'start': 1685951407.2056031, 'stop': 1685951407.206231, '$report_type': 'TestReport', 'item_index': 93, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo['bar'].baz)--zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['bar'].baz)--zab1]"), 'keywords': {"test_expression_interpolate[-$(foo['bar'].baz)--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].baz)--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0009322329997303314, 'start': 1685951407.206868, 'stop': 1685951407.207802, '$report_type': 'TestReport', 'item_index': 93, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo['bar'].baz)--zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['bar'].baz)--zab1]"), 'keywords': {"test_expression_interpolate[-$(foo['bar'].baz)--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].baz)--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000552557999981218, 'start': 1685951407.2088041, 'stop': 1685951407.2093592, '$report_type': 'TestReport', 'item_index': 93, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(.foo["bar"])-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(.foo["bar"])-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]'), 'keywords': {'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003592429993659607, 'start': 1685951407.199389, 'stop': 1685951407.19975, '$report_type': 'TestReport', 'item_index': 110, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]'), 'keywords': {'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["baz"])--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006765959997210302, 'start': 1685951407.210711, 'stop': 1685951407.21139, '$report_type': 'TestReport', 'item_index': 94, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +rker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]'), 'keywords': {'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["baz"])--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005387009996411507, 'start': 1685951407.211931, 'stop': 1685951407.212471, '$report_type': 'TestReport', 'item_index': 94, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]'), 'keywords': {'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["baz"])--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00042146399937337264, 'start': 1685951407.213145, 'stop': 1685951407.213568, '$report_type': 'TestReport', 'item_index': 94, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo)-expected0]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo)-expected0]'), 'keywords': {'test_expression_interpolate[$(foo)-expected0]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo)-expected0': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011265600005572196, 'start': 1685951407.206899, 'stop': 1685951407.2080278, '$report_type': 'TestReport', 'item_index': 74, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo)-expected0]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo)-expected0]'), 'keywords': {'test_expression_interpolate[$(foo)-expected0]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo)-expected0': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005183399998713867, 'start': 1685951407.208926, 'stop': 1685951407.209447, '$report_type': 'TestReport', 'item_index': 74, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo)-expected0]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo)-expected0]'), 'keywords': {'test_expression_interpolate[$(foo)-expected0]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo)-expected0': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004577629997584154, 'start': 1685951407.210113, 'stop': 1685951407.210572, '$report_type': 'TestReport', 'item_index': 74, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]'), 'keywords': {'test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005979940006000106, 'start': 1685951407.200851, 'stop': 1685951407.2014499, '$report_type': 'TestReport', 'item_index': 111, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo.bar['baz'])--zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo.bar['baz'])--zab1]"), 'keywords': {"test_expression_interpolate[-$(foo.bar['baz'])--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['baz'])--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006634139999732724, 'start': 1685951407.2148, 'stop': 1685951407.215465, '$report_type': 'TestReport', 'item_index': 95, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo.bar['baz'])--zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo.bar['baz'])--zab1]"), 'keywords': {"test_expression_interpolate[-$(foo.bar['baz'])--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['baz'])--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004197429998384905, 'start': 1685951407.215997, 'stop': 1685951407.216418, '$report_type': 'TestReport', 'item_index': 95, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar)-expected1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar)-expected1]'), 'keywords': {'test_expression_interpolate[$(foo.bar)-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar)-expected1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006716059997415869, 'start': 1685951407.212064, 'stop': 1685951407.212738, '$report_type': 'TestReport', 'item_index': 75, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo.bar['baz'])--zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo.bar['baz'])--zab1]"), 'keywords': {"test_expression_interpolate[-$(foo.bar['baz'])--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['baz'])--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000442792000285408, 'start': 1685951407.216977, 'stop': 1685951407.217422, '$report_type': 'TestReport', 'item_index': 95, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar)-expected1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar)-expected1]'), 'keywords': {'test_expression_interpolate[$(foo.bar)-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar)-expected1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005192469998291926, 'start': 1685951407.21331, 'stop': 1685951407.213832, '$report_type': 'TestReport', 'item_index': 75, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar)-expected1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar)-expected1]'), 'keywords': {'test_expression_interpolate[$(foo.bar)-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar)-expected1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003980490000685677, 'start': 1685951407.214459, 'stop': 1685951407.214859, '$report_type': 'TestReport', 'item_index': 75, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo ["bar"])-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo ["bar"])-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo['b ar'].baz)--2]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b ar'].baz)--2]"), 'keywords': {"test_expression_interpolate[-$(foo['b ar'].baz)--2]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b ar'].baz)--2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009374299997944036, 'start': 1685951407.218892, 'stop': 1685951407.219831, '$report_type': 'TestReport', 'item_index': 96, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo['b ar'].baz)--2]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b ar'].baz)--2]"), 'keywords': {"test_expression_interpolate[-$(foo['b ar'].baz)--2]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b ar'].baz)--2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0007132060000003548, 'start': 1685951407.2205179, 'stop': 1685951407.2212322, '$report_type': 'TestReport', 'item_index': 96, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo['b ar'].baz)--2]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b ar'].baz)--2]"), 'keywords': {"test_expression_interpolate[-$(foo['b ar'].baz)--2]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b ar'].baz)--2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003877219996866188, 'start': 1685951407.221826, 'stop': 1685951407.222215, '$report_type': 'TestReport', 'item_index': 96, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'])-expected2]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'])-expected2]"), 'keywords': {"test_expression_interpolate[$(foo['bar'])-expected2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'])-expected2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000554790000023786, 'start': 1685951407.216011, 'stop': 1685951407.216567, '$report_type': 'TestReport', 'item_index': 76, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'])-expected2]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'])-expected2]"), 'keywords': {"test_expression_interpolate[$(foo['bar'])-expected2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'])-expected2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004375460002847831, 'start': 1685951407.217064, 'stop': 1685951407.217504, '$report_type': 'TestReport', 'item_index': 76, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'])-expected2]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'])-expected2]"), 'keywords': {"test_expression_interpolate[$(foo['bar'])-expected2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'])-expected2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005313919991749572, 'start': 1685951407.2183092, 'stop': 1685951407.218842, '$report_type': 'TestReport', 'item_index': 76, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]"), 'keywords': {"test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b\\\\'ar'].baz)--true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005959359996268176, 'start': 1685951407.223624, 'stop': 1685951407.224222, '$report_type': 'TestReport', 'item_index': 97, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]"), 'keywords': {"test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b\\\\'ar'].baz)--true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005113509996590437, 'start': 1685951407.224708, 'stop': 1685951407.2252212, '$report_type': 'TestReport', 'item_index': 97, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]"), 'keywords': {"test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b\\\\'ar'].baz)--true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004751559999931487, 'start': 1685951407.22574, 'stop': 1685951407.226217, '$report_type': 'TestReport', 'item_index': 97, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]'), 'keywords': {'test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].baz)--true': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012957270000697463, 'start': 1685951407.228095, 'stop': 1685951407.2293959, '$report_type': 'TestReport', 'item_index': 98, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]'), 'keywords': {'test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].baz)--true': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006754670002919738, 'start': 1685951407.2301362, 'stop': 1685951407.230814, '$report_type': 'TestReport', 'item_index': 98, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]'), 'keywords': {'test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].baz)--true': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005062270001872093, 'start': 1685951407.231463, 'stop': 1685951407.231971, '$report_type': 'TestReport', 'item_index': 98, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["bar"])-expected3]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"])-expected3]'), 'keywords': {'test_expression_interpolate[$(foo["bar"])-expected3]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["bar"])-expected3': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007190819997049402, 'start': 1685951407.2203462, 'stop': 1685951407.221067, '$report_type': 'TestReport', 'item_index': 77, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["bar"])-expected3]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"])-expected3]'), 'keywords': {'test_expression_interpolate[$(foo["bar"])-expected3]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["bar"])-expected3': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00031321599999500904, 'start': 1685951407.221627, 'stop': 1685951407.221941, '$report_type': 'TestReport', 'item_index': 77, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["bar"])-expected3]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"])-expected3]'), 'keywords': {'test_expression_interpolate[$(foo["bar"])-expected3]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["bar"])-expected3': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00025254200045310427, 'start': 1685951407.2223349, 'stop': 1685951407.2225878, '$report_type': 'TestReport', 'item_index': 77, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz)-zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz)-zab1]'), 'keywords': {'test_expression_interpolate[$(foo.bar.baz)-zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz)-zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005453000003399211, 'start': 1685951407.2236989, 'stop': 1685951407.224246, '$report_type': 'TestReport', 'item_index': 78, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz)-zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz)-zab1]'), 'keywords': {'test_expression_interpolate[$(foo.bar.baz)-zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz)-zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00036755200017069, 'start': 1685951407.2247438, 'stop': 1685951407.225114, '$report_type': 'TestReport', 'item_index': 78, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz)-zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz)-zab1]'), 'keywords': {'test_expression_interpolate[$(foo.bar.baz)-zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz)-zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006397089991878602, 'start': 1685951407.2256231, 'stop': 1685951407.2262652, '$report_type': 'TestReport', 'item_index': 78, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\'ar'].baz)-True] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo ["bar"])-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo ["bar"])-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\'ar'].baz)-True] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[( foo["bar"])-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[( foo["bar"])-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo["b'ar"].baz)-True] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\'ar"].baz)-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo["b'ar"].baz)-True] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\'ar"].baz)-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\"ar'].baz)-None] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[( foo["bar"])-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[( foo["bar"])-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo[bar].baz)-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo[bar].baz)-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\"ar'].baz)-None] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo[bar].baz)-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo[bar].baz)-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(lst[0])-A] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst[0])-A]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar"].baz)-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo[\'bar"].baz)-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(lst[0])-A] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst[0])-A]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(lst[1])-B] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst[1])-B]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar']["baz"]) $(foo['bar']["baz"])-zab1 zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar"].baz)-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo[\'bar"].baz)-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar].baz)-False] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar].baz)-False]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]'), 'keywords': {'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].baz)--null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001641023999582103, 'start': 1685951407.2567759, 'stop': 1685951407.258422, '$report_type': 'TestReport', 'item_index': 99, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(lst[1])-B] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst[1])-B]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz)-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz)-zab1]"), 'keywords': {"test_expression_interpolate[$(foo['bar'].baz)-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz)-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011922129997401498, 'start': 1685951407.258692, 'stop': 1685951407.2599082, '$report_type': 'TestReport', 'item_index': 79, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]'), 'keywords': {'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].baz)--null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000932054000259086, 'start': 1685951407.2593322, 'stop': 1685951407.260267, '$report_type': 'TestReport', 'item_index': 99, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(lst.length)-2] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst.length)-2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz)-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz)-zab1]"), 'keywords': {"test_expression_interpolate[$(foo['bar'].baz)-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz)-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005645649998768931, 'start': 1685951407.260633, 'stop': 1685951407.2612, '$report_type': 'TestReport', 'item_index': 79, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]'), 'keywords': {'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].baz)--null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00041843700000754325, 'start': 1685951407.260957, 'stop': 1685951407.261378, '$report_type': 'TestReport', 'item_index': 99, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar']["baz"]) $(foo['bar']["baz"])-zab1 zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz)-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz)-zab1]"), 'keywords': {"test_expression_interpolate[$(foo['bar'].baz)-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz)-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005214060001890175, 'start': 1685951407.261953, 'stop': 1685951407.2624772, '$report_type': 'TestReport', 'item_index': 79, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]'), 'keywords': {'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']["bazz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004066560004503117, 'start': 1685951407.2626, 'stop': 1685951407.263008, '$report_type': 'TestReport', 'item_index': 160, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]'), 'keywords': {'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']["bazz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005061390002083499, 'start': 1685951407.264887, 'stop': 1685951407.265397, '$report_type': 'TestReport', 'item_index': 160, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b\\\\'ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006696979999105679, 'start': 1685951407.2652879, 'stop': 1685951407.265959, '$report_type': 'TestReport', 'item_index': 177, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b\\\\'ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005427820005934336, 'start': 1685951407.2666292, 'stop': 1685951407.267174, '$report_type': 'TestReport', 'item_index': 177, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]"), 'keywords': {"test_expression_interpolate_failures[$(foo.bar['bazz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['bazz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005516640003406792, 'start': 1685951407.2671092, 'stop': 1685951407.267663, '$report_type': 'TestReport', 'item_index': 161, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]', 'tests/test_examples.py::test_expression_interpolate_failures[$(fooz)]', 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.barz)]', "tests/test_examples.py::test_expression_interpolate_failures[$(foo['barz'])]", 'tests/test_examples.py::test_expression_interpolate_failures[$(foo["barz"])]', 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar.bazz)]', "tests/test_examples.py::test_expression_interpolate_failures[$(foo['bar'].bazz)]", 'tests/test_examples.py::test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]', "tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])]", "tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]", 'tests/test_examples.py::test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]', 'tests/test_examples.py::test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]', 'tests/test_examples.py::test_e pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006098329995438689, 'start': 1685951407.268758, 'stop': 1685951407.26937, '$report_type': 'TestReport', 'item_index': 178, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]"), 'keywords': {"test_expression_interpolate_failures[$(foo.bar['bazz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['bazz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006548279998241924, 'start': 1685951407.2683752, 'stop': 1685951407.269032, '$report_type': 'TestReport', 'item_index': 161, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]"), 'keywords': {"test_expression_interpolate_failures[$(foo.bar['bazz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['bazz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00042578600005072076, 'start': 1685951407.269708, 'stop': 1685951407.270136, '$report_type': 'TestReport', 'item_index': 161, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005757959997936268, 'start': 1685951407.269971, 'stop': 1685951407.270549, '$report_type': 'TestReport', 'item_index': 178, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004131420000703656, 'start': 1685951407.2712471, 'stop': 1685951407.271662, '$report_type': 'TestReport', 'item_index': 178, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005706130004909937, 'start': 1685951407.2716181, 'stop': 1685951407.272191, '$report_type': 'TestReport', 'item_index': 162, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar].baz)-False] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar].baz)-False]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0009290719999626162, 'start': 1685951407.272831, 'stop': 1685951407.2737632, '$report_type': 'TestReport', 'item_index': 162, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(lst.length)-2] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst.length)-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007420629999614903, 'start': 1685951407.273581, 'stop': 1685951407.274325, '$report_type': 'TestReport', 'item_index': 179, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006088889995226054, 'start': 1685951407.27457, 'stop': 1685951407.275181, '$report_type': 'TestReport', 'item_index': 162, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]") + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006789319995732512, 'start': 1685951407.275402, 'stop': 1685951407.276083, '$report_type': 'TestReport', 'item_index': 179, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[{foo}-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[{foo}-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004388759998619207, 'start': 1685951407.2767649, 'stop': 1685951407.277206, '$report_type': 'TestReport', 'item_index': 179, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\'ar"].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008408160001636134, 'start': 1685951407.2767282, 'stop': 1685951407.277571, '$report_type': 'TestReport', 'item_index': 163, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\'ar"].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004004479997092858, 'start': 1685951407.278184, 'stop': 1685951407.2785861, '$report_type': 'TestReport', 'item_index': 163, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006830409993199282, 'start': 1685951407.2786229, 'stop': 1685951407.279308, '$report_type': 'TestReport', 'item_index': 180, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\'ar"].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003820450001512654, 'start': 1685951407.279045, 'stop': 1685951407.2794292, '$report_type': 'TestReport', 'item_index': 163, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(lst['length'])-2] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(lst['length'])-2]") + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006137039999885019, 'start': 1685951407.280024, 'stop': 1685951407.28064, '$report_type': 'TestReport', 'item_index': 180, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006067779995646561, 'start': 1685951407.2811599, 'stop': 1685951407.281769, '$report_type': 'TestReport', 'item_index': 164, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005609320005532936, 'start': 1685951407.28135, 'stop': 1685951407.281912, '$report_type': 'TestReport', 'item_index': 180, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005678549996446236, 'start': 1685951407.2823832, 'stop': 1685951407.282953, '$report_type': 'TestReport', 'item_index': 164, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000394663000406581, 'start': 1685951407.2837, 'stop': 1685951407.284096, '$report_type': 'TestReport', 'item_index': 164, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008642109996799263, 'start': 1685951407.283328, 'stop': 1685951407.284194, '$report_type': 'TestReport', 'item_index': 181, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006055339999875287, 'start': 1685951407.2848902, 'stop': 1685951407.2854981, '$report_type': 'TestReport', 'item_index': 181, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(lst[O])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[O])]'), 'keywords': {'test_expression_interpolate_failures[$(lst[O])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[O])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003800060003413819, 'start': 1685951407.285238, 'stop': 1685951407.285619, '$report_type': 'TestReport', 'item_index': 165, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005741320001106942, 'start': 1685951407.286174, 'stop': 1685951407.2867498, '$report_type': 'TestReport', 'item_index': 181, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(lst[O])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[O])]'), 'keywords': {'test_expression_interpolate_failures[$(lst[O])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[O])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00043068799914181, 'start': 1685951407.2861109, 'stop': 1685951407.2865438, '$report_type': 'TestReport', 'item_index': 165, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(lst[O])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[O])]'), 'keywords': {'test_expression_interpolate_failures[$(lst[O])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[O])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005541370001083123, 'start': 1685951407.287271, 'stop': 1685951407.2878258, '$report_type': 'TestReport', 'item_index': 165, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[{foo}-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[{foo}-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(lst[2])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[2])]'), 'keywords': {'test_expression_interpolate_failures[$(lst[2])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[2])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005359009992389474, 'start': 1685951407.289239, 'stop': 1685951407.289776, '$report_type': 'TestReport', 'item_index': 166, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(lst[2])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[2])]'), 'keywords': {'test_expression_interpolate_failures[$(lst[2])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[2])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004137679998166277, 'start': 1685951407.290252, 'stop': 1685951407.290667, '$report_type': 'TestReport', 'item_index': 166, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000969509999777074, 'start': 1685951407.288249, 'stop': 1685951407.289221, '$report_type': 'TestReport', 'item_index': 182, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004434610000316752, 'start': 1685951407.289933, 'stop': 1685951407.290378, '$report_type': 'TestReport', 'item_index': 182, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(lst[2])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[2])]'), 'keywords': {'test_expression_interpolate_failures[$(lst[2])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[2])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00047978200018405914, 'start': 1685951407.29133, 'stop': 1685951407.2918122, '$report_type': 'TestReport', 'item_index': 166, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005843660001119133, 'start': 1685951407.291046, 'stop': 1685951407.2916322, '$report_type': 'TestReport', 'item_index': 182, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(lst.lengthz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst.lengthz)]'), 'keywords': {'test_expression_interpolate_failures[$(lst.lengthz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst.lengthz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005679960004272289, 'start': 1685951407.293067, 'stop': 1685951407.293637, '$report_type': 'TestReport', 'item_index': 167, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(lst.lengthz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst.lengthz)]'), 'keywords': {'test_expression_interpolate_failures[$(lst.lengthz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst.lengthz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0007167959993239492, 'start': 1685951407.2943182, 'stop': 1685951407.295038, '$report_type': 'TestReport', 'item_index': 167, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008366640004169312, 'start': 1685951407.29308, 'stop': 1685951407.293918, '$report_type': 'TestReport', 'item_index': 183, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(lst['length'])-2] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(lst['length'])-2]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0008976100007203058, 'start': 1685951407.294513, 'stop': 1685951407.295413, '$report_type': 'TestReport', 'item_index': 183, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(lst.lengthz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst.lengthz)]'), 'keywords': {'test_expression_interpolate_failures[$(lst.lengthz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst.lengthz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00043911000011576107, 'start': 1685951407.295819, 'stop': 1685951407.296261, '$report_type': 'TestReport', 'item_index': 167, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000552768000488868, 'start': 1685951407.296146, 'stop': 1685951407.296701, '$report_type': 'TestReport', 'item_index': 183, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(lst['lengthz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(lst['lengthz'])]"), 'keywords': {"test_expression_interpolate_failures[$(lst['lengthz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(lst['lengthz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005254800007605809, 'start': 1685951407.297803, 'stop': 1685951407.29833, '$report_type': 'TestReport', 'item_index': 168, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-$foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008985060003396939, 'start': 1685951407.298087, 'stop': 1685951407.298988, '$report_type': 'TestReport', 'item_index': 184, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(lst['lengthz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(lst['lengthz'])]"), 'keywords': {"test_expression_interpolate_failures[$(lst['lengthz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(lst['lengthz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0007137029997466016, 'start': 1685951407.29904, 'stop': 1685951407.299756, '$report_type': 'TestReport', 'item_index': 168, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-$foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00045144300020183437, 'start': 1685951407.299617, 'stop': 1685951407.3000698, '$report_type': 'TestReport', 'item_index': 184, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(lst['lengthz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(lst['lengthz'])]"), 'keywords': {"test_expression_interpolate_failures[$(lst['lengthz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(lst['lengthz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004480620000322233, 'start': 1685951407.30042, 'stop': 1685951407.30087, '$report_type': 'TestReport', 'item_index': 168, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-$foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005127379999976256, 'start': 1685951407.3006878, 'stop': 1685951407.3012018, '$report_type': 'TestReport', 'item_index': 184, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]") + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo.barz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.barz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo.barz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.barz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012037999995300197, 'start': 1685951407.3027682, 'stop': 1685951407.303977, '$report_type': 'TestReport', 'item_index': 169, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\foo-foo-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-foo-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\foo-foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012132620004194905, 'start': 1685951407.3032231, 'stop': 1685951407.304441, '$report_type': 'TestReport', 'item_index': 185, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo.barz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.barz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo.barz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.barz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005943220003246097, 'start': 1685951407.304916, 'stop': 1685951407.305512, '$report_type': 'TestReport', 'item_index': 169, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo.barz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.barz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo.barz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.barz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005169820005903603, 'start': 1685951407.306241, 'stop': 1685951407.306761, '$report_type': 'TestReport', 'item_index': 169, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\foo-foo-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-foo-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\foo-foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005905620000703493, 'start': 1685951407.305322, 'stop': 1685951407.3059158, '$report_type': 'TestReport', 'item_index': 185, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] +t[O])]'), 'keywords': {'test_expression_interpolate_failures[$(lst[O])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(lst[O])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'lon pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\foo-foo-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-foo-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\foo-foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006867839992992231, 'start': 1685951407.306574, 'stop': 1685951407.307263, '$report_type': 'TestReport', 'item_index': 185, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['barz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['barz'])]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['barz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['barz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006969249998292071, 'start': 1685951407.308523, 'stop': 1685951407.309222, '$report_type': 'TestReport', 'item_index': 170, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\x-x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\x-x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\x-x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\x-x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012723529998766026, 'start': 1685951407.308836, 'stop': 1685951407.310111, '$report_type': 'TestReport', 'item_index': 186, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['barz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['barz'])]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['barz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['barz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006792459998905542, 'start': 1685951407.3099258, 'stop': 1685951407.310608, '$report_type': 'TestReport', 'item_index': 170, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\x-x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\x-x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\x-x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\x-x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005959199997960241, 'start': 1685951407.310878, 'stop': 1685951407.311477, '$report_type': 'TestReport', 'item_index': 186, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['barz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['barz'])]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['barz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['barz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006702830005451688, 'start': 1685951407.311449, 'stop': 1685951407.3121212, '$report_type': 'TestReport', 'item_index': 170, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\x-x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\x-x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\x-x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\x-x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005147210003997316, 'start': 1685951407.312405, 'stop': 1685951407.312922, '$report_type': 'TestReport', 'item_index': 186, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[foo.bar)-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[foo.bar)-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[foo.b ar)-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[foo.b ar)-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo["barz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["barz"])]'), 'keywords': {'test_expression_interpolate_failures[-$(foo["barz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["barz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004518999994616024, 'start': 1685951407.313341, 'stop': 1685951407.313795, '$report_type': 'TestReport', 'item_index': 171, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo["barz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["barz"])]'), 'keywords': {'test_expression_interpolate_failures[-$(foo["barz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["barz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0009783209998204256, 'start': 1685951407.314529, 'stop': 1685951407.31551, '$report_type': 'TestReport', 'item_index': 171, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001006874999802676, 'start': 1685951407.314362, 'stop': 1685951407.315371, '$report_type': 'TestReport', 'item_index': 187, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo["barz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["barz"])]'), 'keywords': {'test_expression_interpolate_failures[-$(foo["barz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["barz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004024009995191591, 'start': 1685951407.316164, 'stop': 1685951407.3165681, '$report_type': 'TestReport', 'item_index': 171, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004070799996043206, 'start': 1685951407.31598, 'stop': 1685951407.316389, '$report_type': 'TestReport', 'item_index': 187, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005338979999578441, 'start': 1685951407.317007, 'stop': 1685951407.317543, '$report_type': 'TestReport', 'item_index': 187, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[foo.b ar)-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[foo.b ar)-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar.bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.bar.bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo.bar.bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007865879997552838, 'start': 1685951407.318114, 'stop': 1685951407.3189042, '$report_type': 'TestReport', 'item_index': 172, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar.bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.bar.bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo.bar.bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005756250002377783, 'start': 1685951407.319585, 'stop': 1685951407.320163, '$report_type': 'TestReport', 'item_index': 172, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008858649998728652, 'start': 1685951407.3192792, 'stop': 1685951407.3201668, '$report_type': 'TestReport', 'item_index': 188, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar.bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.bar.bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo.bar.bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000410487000408466, 'start': 1685951407.320811, 'stop': 1685951407.321223, '$report_type': 'TestReport', 'item_index': 172, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00044027899912180146, 'start': 1685951407.32071, 'stop': 1685951407.321152, '$report_type': 'TestReport', 'item_index': 188, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} +rize': 1, 'pytestmark': 1, '$(lst[O])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'lonrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00043068799914181, 'start': 1685951407.2861109, 'stop': 1685951407.2865438, '$report_type': 'TestReport', 'item_index': 165, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} +pV£À3§Höãy`1V°V£4§Äf£ÊÊËp6M`4§i./? ÞðV£ finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004889510000793962, 'start': 1685951407.321783, 'stop': 1685951407.322273, '$report_type': 'TestReport', 'item_index': 188, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['bar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['bar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006149490000098012, 'start': 1685951407.3226628, 'stop': 1685951407.3232799, '$report_type': 'TestReport', 'item_index': 173, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['bar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['bar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005227310002737795, 'start': 1685951407.3238761, 'stop': 1685951407.324401, '$report_type': 'TestReport', 'item_index': 173, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008435240006292588, 'start': 1685951407.323806, 'stop': 1685951407.324651, '$report_type': 'TestReport', 'item_index': 189, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['bar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['bar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005881890001546708, 'start': 1685951407.325191, 'stop': 1685951407.325781, '$report_type': 'TestReport', 'item_index': 173, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000570602999687253, 'start': 1685951407.325197, 'stop': 1685951407.32577, '$report_type': 'TestReport', 'item_index': 189, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004434630000105244, 'start': 1685951407.326494, 'stop': 1685951407.3269398, '$report_type': 'TestReport', 'item_index': 189, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]'), 'keywords': {'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["bazz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000519357000484888, 'start': 1685951407.327293, 'stop': 1685951407.3278148, '$report_type': 'TestReport', 'item_index': 174, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000679273999594443, 'start': 1685951407.32805, 'stop': 1685951407.3287308, '$report_type': 'TestReport', 'item_index': 190, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]'), 'keywords': {'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["bazz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004676630005633342, 'start': 1685951407.328387, 'stop': 1685951407.328856, '$report_type': 'TestReport', 'item_index': 174, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003356179995535058, 'start': 1685951407.329217, 'stop': 1685951407.3295538, '$report_type': 'TestReport', 'item_index': 190, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]'), 'keywords': {'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["bazz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00038859100004629, 'start': 1685951407.32945, 'stop': 1685951407.3298402, '$report_type': 'TestReport', 'item_index': 174, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004107869999643299, 'start': 1685951407.3301141, 'stop': 1685951407.3305259, '$report_type': 'TestReport', 'item_index': 190, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['bar'])--{"baz": "zab1"}] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar['bazz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo.bar['bazz'])]"), 'keywords': {"test_expression_interpolate_failures[-$(foo.bar['bazz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['bazz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008235509994847234, 'start': 1685951407.331155, 'stop': 1685951407.33198, '$report_type': 'TestReport', 'item_index': 175, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[foo.b'ar)-False] + location: ('tests/test_examples.py', 64, "test_expression_match[foo.b'ar)-False]") + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009039380001922837, 'start': 1685951407.3321338, 'stop': 1685951407.3330402, '$report_type': 'TestReport', 'item_index': 191, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar['bazz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo.bar['bazz'])]"), 'keywords': {"test_expression_interpolate_failures[-$(foo.bar['bazz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['bazz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006024900003467337, 'start': 1685951407.332716, 'stop': 1685951407.3333209, '$report_type': 'TestReport', 'item_index': 175, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\'ar'].baz) $(foo['b\\'ar'].baz)-true true] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]") + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005204970002523623, 'start': 1685951407.333714, 'stop': 1685951407.334236, '$report_type': 'TestReport', 'item_index': 191, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar['bazz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo.bar['bazz'])]"), 'keywords': {"test_expression_interpolate_failures[-$(foo.bar['bazz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['bazz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00038296000002446817, 'start': 1685951407.333898, 'stop': 1685951407.334283, '$report_type': 'TestReport', 'item_index': 175, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00045267499990586657, 'start': 1685951407.3348422, 'stop': 1685951407.335295, '$report_type': 'TestReport', 'item_index': 191, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['bar'])--{"baz": "zab1"}] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[foo.b'ar)-False] + location: ('tests/test_examples.py', 64, "test_expression_match[foo.b'ar)-False]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo+bar-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo+bar-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo.bar.baz)--zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar.baz)--zab1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\'ar'].baz) $(foo['b\\'ar'].baz)-true true] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo+bar-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo+bar-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo["b\\'ar"].baz) $(foo["b\\'ar"].baz)-true true] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo bar-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo bar-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo["b\\'ar"].baz) $(foo["b\\'ar"].baz)-true true] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\"ar'].baz) $(foo['b\\"ar'].baz)-null null] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo.bar.baz)--zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar.baz)--zab1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['bar'].baz)--zab1] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['bar'].baz)--zab1]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['bar'].baz)--zab1] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['bar'].baz)--zab1]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['bar']["baz"])--zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\"ar'].baz) $(foo['b\\"ar'].baz)-null null] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['bar']["baz"])--zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo bar-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo bar-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo)-expected0] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo)-expected0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b'ar":{"baz":true},"b\\"ar":{"baz":null}}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo)-expected0] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo)-expected0]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo.bar['baz'])--zab1] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo.bar['baz'])--zab1]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar)-expected1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar)-expected1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo.bar['baz'])--zab1] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo.bar['baz'])--zab1]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['b ar'].baz)--2] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b ar'].baz)--2]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar)-expected1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar)-expected1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['b ar'].baz)--2] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b ar'].baz)--2]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar'])-expected2] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'])-expected2]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['b\\'ar'].baz)--true] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['b\\'ar'].baz)--true] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo["b\\'ar"].baz)--true] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar'])-expected2] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'])-expected2]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo["bar"])-expected3] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"])-expected3]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo["b\\'ar"].baz)--true] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo["bar"])-expected3] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"])-expected3]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz)-zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz)-zab1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz)-zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz)-zab1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['b\\"ar'].baz)--null] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz)-zab1] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz)-zab1]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['b\\"ar'].baz)--null] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz)-zab1] + location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz)-zab1]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['bar']["bazz"])] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\'ar'].bazz)] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\'ar'].bazz)] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['bar']["bazz"])] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\'ar"].bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\'ar'].bazz)] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\'ar"].bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\"ar'].bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\'ar'].bazz)] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo["b'ar"].bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\"ar'].bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$(foo.bar.baz)-$(foo.bar.baz)-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\x-x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.21595973200055596, 'start': 1685951407.1566231, 'stop': 1685951407.372582, '$report_type': 'TestReport', 'item_index': 140, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo['b\\\\'ar'].baz)--true]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['b\\\\'ar'].baz)--true]"), 'keywords': {"test_parameter_to_expression[-$(foo['b\\\\'ar'].baz)--true]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b\\\\'ar'].baz)--true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.2159330200001932, 'start': 1685951407.1566021, 'stop': 1685951407.372535, '$report_type': 'TestReport', 'item_index': 120, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo['b\\\\'ar'].baz)--true]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['b\\\\'ar'].baz)--true]"), 'keywords': {"test_parameter_to_expression[-$(foo['b\\\\'ar'].baz)--true]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b\\\\'ar'].baz)--true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0009504660001766752, 'start': 1685951407.374021, 'stop': 1685951407.374974, '$report_type': 'TestReport', 'item_index': 120, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012882950004495797, 'start': 1685951407.373827, 'stop': 1685951407.3751192, '$report_type': 'TestReport', 'item_index': 192, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\x-x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0013115470001139329, 'start': 1685951407.374101, 'stop': 1685951407.375416, '$report_type': 'TestReport', 'item_index': 140, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003900869996869005, 'start': 1685951407.375917, 'stop': 1685951407.376309, '$report_type': 'TestReport', 'item_index': 192, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo["b'ar"].bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00034418100040056743, 'start': 1685951407.3768342, 'stop': 1685951407.3771799, '$report_type': 'TestReport', 'item_index': 192, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]'), 'keywords': {'test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].baz)--true': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006808329999330454, 'start': 1685951407.376863, 'stop': 1685951407.3775449, '$report_type': 'TestReport', 'item_index': 121, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\"ar'].bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007626679998793406, 'start': 1685951407.3771882, 'stop': 1685951407.377953, '$report_type': 'TestReport', 'item_index': 141, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_trick_scandeps', 'location': ('tests/test_examples.py', 549, 'test_trick_scandeps'), 'keywords': {'test_trick_scandeps': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00019978900036221603, 'start': 1685951407.378159, 'stop': 1685951407.37836, '$report_type': 'TestReport', 'item_index': 209, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$(foo.bar.baz)-$(foo.bar.baz)-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\"ar'].bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-\\zab1-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]'), 'keywords': {'test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].baz)--true': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0029614650002258713, 'start': 1685951407.378196, 'stop': 1685951407.3811588, '$report_type': 'TestReport', 'item_index': 121, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0026735219998954562, 'start': 1685951407.378525, 'stop': 1685951407.3811998, '$report_type': 'TestReport', 'item_index': 141, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00046120299975882517, 'start': 1685951407.38191, 'stop': 1685951407.382373, '$report_type': 'TestReport', 'item_index': 141, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]'), 'keywords': {'test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].baz)--true': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005465459998958977, 'start': 1685951407.3817651, 'stop': 1685951407.3823118, '$report_type': 'TestReport', 'item_index': 121, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].baz)--null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004650689998015878, 'start': 1685951407.383429, 'stop': 1685951407.3838952, '$report_type': 'TestReport', 'item_index': 122, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007457429992427933, 'start': 1685951407.383577, 'stop': 1685951407.384324, '$report_type': 'TestReport', 'item_index': 142, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst[O])] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[O])]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-\\zab1-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst[O])] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[O])]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].baz)--null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002541908999774023, 'start': 1685951407.3843572, 'stop': 1685951407.386901, '$report_type': 'TestReport', 'item_index': 122, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0024571300000388874, 'start': 1685951407.384916, 'stop': 1685951407.387375, '$report_type': 'TestReport', 'item_index': 142, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].baz)--null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003885379992425442, 'start': 1685951407.387537, 'stop': 1685951407.387927, '$report_type': 'TestReport', 'item_index': 122, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['b ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005136209992997465, 'start': 1685951407.386643, 'stop': 1685951407.387158, '$report_type': 'TestReport', 'item_index': 176, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst[2])] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[2])]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005822630000693607, 'start': 1685951407.3891551, 'stop': 1685951407.389739, '$report_type': 'TestReport', 'item_index': 123, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000855311000123038, 'start': 1685951407.38975, 'stop': 1685951407.3906062, '$report_type': 'TestReport', 'item_index': 143, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['b ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00047023500064824475, 'start': 1685951407.3877409, 'stop': 1685951407.388213, '$report_type': 'TestReport', 'item_index': 176, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['b ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000362337000296975, 'start': 1685951407.3888772, 'stop': 1685951407.389241, '$report_type': 'TestReport', 'item_index': 176, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type1-sink_type1-None-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type1-sink_type1-None-None-warning]'), 'keywords': {'test_typechecking[src_type1-sink_type1-None-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type1-sink_type1-None-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001482418999330548, 'start': 1685951407.3904798, 'stop': 1685951407.391967, '$report_type': 'TestReport', 'item_index': 224, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} +sts/test_examples.py::test_parameter_to_expression_inter`¬\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'tests/test_examples.py::°[usion_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo÷Kst_examples.py::test_parameter_to_expression_interpolate¬$(foo.bar.baz)-\\\\zab1-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]', 'testÚamples.Úparameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[ finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type1-sink_type1-None-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type1-sink_type1-None-None-warning]'), 'keywords': {'test_typechecking[src_type1-sink_type1-None-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type1-sink_type1-None-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004413639999256702, 'start': 1685951407.392577, 'stop': 1685951407.39302, '$report_type': 'TestReport', 'item_index': 224, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.003042719000404759, 'start': 1685951407.3904269, 'stop': 1685951407.393472, '$report_type': 'TestReport', 'item_index': 123, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type1-sink_type1-None-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type1-sink_type1-None-None-warning]'), 'keywords': {'test_typechecking[src_type1-sink_type1-None-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type1-sink_type1-None-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00045084499924996635, 'start': 1685951407.393543, 'stop': 1685951407.393995, '$report_type': 'TestReport', 'item_index': 224, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00042707000011432683, 'start': 1685951407.394169, 'stop': 1685951407.394598, '$report_type': 'TestReport', 'item_index': 123, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0027749270002459525, 'start': 1685951407.3911512, 'stop': 1685951407.393929, '$report_type': 'TestReport', 'item_index': 143, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type2-sink_type2-None-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type2-sink_type2-None-None-exception]'), 'keywords': {'test_typechecking[src_type2-sink_type2-None-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type2-sink_type2-None-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007488389992431621, 'start': 1685951407.395227, 'stop': 1685951407.3959758, '$report_type': 'TestReport', 'item_index': 225, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type2-sink_type2-None-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type2-sink_type2-None-None-exception]'), 'keywords': {'test_typechecking[src_type2-sink_type2-None-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type2-sink_type2-None-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00038672000027872855, 'start': 1685951407.3965921, 'stop': 1685951407.39698, '$report_type': 'TestReport', 'item_index': 225, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type2-sink_type2-None-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type2-sink_type2-None-None-exception]'), 'keywords': {'test_typechecking[src_type2-sink_type2-None-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type2-sink_type2-None-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00036709400046675, 'start': 1685951407.397452, 'stop': 1685951407.39782, '$report_type': 'TestReport', 'item_index': 225, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007763550001982367, 'start': 1685951407.396468, 'stop': 1685951407.397246, '$report_type': 'TestReport', 'item_index': 144, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst[2])] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[2])]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006835909998699208, 'start': 1685951407.395856, 'stop': 1685951407.3965409, '$report_type': 'TestReport', 'item_index': 124, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst.lengthz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst.lengthz)]') +s/test_examples.py::test_expression_interpolate[-$(foo['bar']["baz"])--zab1] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo bar-False] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo bar-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate[$(foo)-expected0] + location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo)-expected0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: +$(foo['b\\\\'ar'].baz)--true]", 'tests/test_examples.py::test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]', 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baÚ', 't finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\$(foo.bar.baz)-\\$(foo.bar.baz)-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0022234130001379526, 'start': 1685951407.3977652, 'stop': 1685951407.399989, '$report_type': 'TestReport', 'item_index': 144, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0025608940004531178, 'start': 1685951407.397172, 'stop': 1685951407.399735, '$report_type': 'TestReport', 'item_index': 124, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type3-sink_type3-None-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type3-sink_type3-None-None-pass]'), 'keywords': {'test_typechecking[src_type3-sink_type3-None-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type3-sink_type3-None-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009139409994531889, 'start': 1685951407.3989382, 'stop': 1685951407.399853, '$report_type': 'TestReport', 'item_index': 226, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003133230002276832, 'start': 1685951407.400414, 'stop': 1685951407.4007292, '$report_type': 'TestReport', 'item_index': 144, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00038902599953871686, 'start': 1685951407.400353, 'stop': 1685951407.400743, '$report_type': 'TestReport', 'item_index': 124, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type3-sink_type3-None-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type3-sink_type3-None-None-pass]'), 'keywords': {'test_typechecking[src_type3-sink_type3-None-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type3-sink_type3-None-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003926070003217319, 'start': 1685951407.40034, 'stop': 1685951407.400734, '$report_type': 'TestReport', 'item_index': 226, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type3-sink_type3-None-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type3-sink_type3-None-None-pass]'), 'keywords': {'test_typechecking[src_type3-sink_type3-None-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type3-sink_type3-None-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005393129995354684, 'start': 1685951407.4012449, 'stop': 1685951407.401786, '$report_type': 'TestReport', 'item_index': 226, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005235139997239457, 'start': 1685951407.4018528, 'stop': 1685951407.402378, '$report_type': 'TestReport', 'item_index': 125, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005191010004637064, 'start': 1685951407.401671, 'stop': 1685951407.4021912, '$report_type': 'TestReport', 'item_index': 145, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type4-sink_type4-None-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type4-sink_type4-None-None-warning]'), 'keywords': {'test_typechecking[src_type4-sink_type4-None-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type4-sink_type4-None-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009563419998812606, 'start': 1685951407.40286, 'stop': 1685951407.403818, '$report_type': 'TestReport', 'item_index': 227, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type4-sink_type4-None-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type4-sink_type4-None-None-warning]'), 'keywords': {'test_typechecking[src_type4-sink_type4-None-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type4-sink_type4-None-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004525889999058563, 'start': 1685951407.404313, 'stop': 1685951407.404767, '$report_type': 'TestReport', 'item_index': 227, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0021481710000443854, 'start': 1685951407.402588, 'stop': 1685951407.404737, '$report_type': 'TestReport', 'item_index': 145, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002644731000145839, 'start': 1685951407.402842, 'stop': 1685951407.405488, '$report_type': 'TestReport', 'item_index': 125, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004751659998873947, 'start': 1685951407.405452, 'stop': 1685951407.4059289, '$report_type': 'TestReport', 'item_index': 145, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type4-sink_type4-None-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type4-sink_type4-None-None-warning]'), 'keywords': {'test_typechecking[src_type4-sink_type4-None-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type4-sink_type4-None-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004646380002668593, 'start': 1685951407.405369, 'stop': 1685951407.405837, '$report_type': 'TestReport', 'item_index': 227, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_trick_scandeps', 'location': ('tests/test_examples.py', 549, 'test_trick_scandeps'), 'keywords': {'test_trick_scandeps': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/trick_defaults.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/trick_defaults.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/trick_defaults.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/trick_defaults.cwl'")], 'duration': 0.00035959799970441964, 'start': 1685951407.405083, 'stop': 1685951407.4054441, '$report_type': 'TestReport', 'item_index': 209, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_scandeps_defaults_with_secondaryfiles', 'location': ('tests/test_examples.py', 559, 'test_scandeps_defaults_with_secondaryfiles'), 'keywords': {'test_scandeps_defaults_with_secondaryfiles': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004678010000134236, 'start': 1685951407.406656, 'stop': 1685951407.407125, '$report_type': 'TestReport', 'item_index': 210, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +az": "zab1"} {"baz": "zab1"}]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz)-zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz)-zab1]'), 'keywords': {'test_expression_interpolate[$(foo.bar.baz)-zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz)-zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005453000003399211, 'start': 1685951407.2236989, 'stop': 1685951407.224246, '$report_type': 'TestReport', 'item_index': 78, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +d_basecommand_docker[--parallelPáK pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013709080003536656, 'start': 1685951407.4074838, 'stop': 1685951407.4088588, '$report_type': 'TestReport', 'item_index': 146, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00039958999968803255, 'start': 1685951407.406065, 'stop': 1685951407.406466, '$report_type': 'TestReport', 'item_index': 125, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst.lengthz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst.lengthz)]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type5-sink_type5-None-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type5-sink_type5-None-None-exception]'), 'keywords': {'test_typechecking[src_type5-sink_type5-None-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type5-sink_type5-None-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018181539999204688, 'start': 1685951407.407179, 'stop': 1685951407.4090009, '$report_type': 'TestReport', 'item_index': 228, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type5-sink_type5-None-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type5-sink_type5-None-None-exception]'), 'keywords': {'test_typechecking[src_type5-sink_type5-None-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type5-sink_type5-None-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005446520008263178, 'start': 1685951407.409743, 'stop': 1685951407.4102888, '$report_type': 'TestReport', 'item_index': 228, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst['lengthz'])] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(lst['lengthz'])]") + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]'), 'keywords': {'test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012807740004063817, 'start': 1685951407.408213, 'stop': 1685951407.4094982, '$report_type': 'TestReport', 'item_index': 126, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002835494999999355, 'start': 1685951407.4097111, 'stop': 1685951407.412548, '$report_type': 'TestReport', 'item_index': 146, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type5-sink_type5-None-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type5-sink_type5-None-None-exception]'), 'keywords': {'test_typechecking[src_type5-sink_type5-None-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type5-sink_type5-None-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005952259998593945, 'start': 1685951407.41092, 'stop': 1685951407.411517, '$report_type': 'TestReport', 'item_index': 228, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006266170003073057, 'start': 1685951407.413418, 'stop': 1685951407.414047, '$report_type': 'TestReport', 'item_index': 146, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]'), 'keywords': {'test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004931049998049275, 'start': 1685951407.414334, 'stop': 1685951407.414829, '$report_type': 'TestReport', 'item_index': 126, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]'), 'keywords': {'test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "[worker-gw5] received command runtests {'indices': [193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208]}\n")], 'duration': 0.21252873800040106, 'start': 1685951407.201897, 'stop': 1685951407.4144251, '$report_type': 'TestReport', 'item_index': 111, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type6-sink_type6-merge_nested-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type6-sink_type6-merge_nested-None-exception]'), 'keywords': {'test_typechecking[src_type6-sink_type6-merge_nested-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type6-sink_type6-merge_nested-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001179238999611698, 'start': 1685951407.413032, 'stop': 1685951407.4142132, '$report_type': 'TestReport', 'item_index': 229, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$foo-$foo-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]') + finish pytest_runtest_logstart --> [] [hook] +eport: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\"ar'].bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + fini pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type6-sink_type6-merge_nested-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type6-sink_type6-merge_nested-None-exception]'), 'keywords': {'test_typechecking[src_type6-sink_type6-merge_nested-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type6-sink_type6-merge_nested-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000562311000066984, 'start': 1685951407.414814, 'stop': 1685951407.4153779, '$report_type': 'TestReport', 'item_index': 229, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001313748000029591, 'start': 1685951407.415655, 'stop': 1685951407.416972, '$report_type': 'TestReport', 'item_index': 147, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type6-sink_type6-merge_nested-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type6-sink_type6-merge_nested-None-exception]'), 'keywords': {'test_typechecking[src_type6-sink_type6-merge_nested-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type6-sink_type6-merge_nested-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0008192459999918356, 'start': 1685951407.416242, 'stop': 1685951407.417064, '$report_type': 'TestReport', 'item_index': 229, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]'), 'keywords': {'test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "[worker-gw5] received command runtests {'indices': [193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208]}\n")], 'duration': 0.0010135719994650572, 'start': 1685951407.41607, 'stop': 1685951407.417087, '$report_type': 'TestReport', 'item_index': 111, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]"), 'keywords': {"test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008249689999502152, 'start': 1685951407.41672, 'stop': 1685951407.417547, '$report_type': 'TestReport', 'item_index': 127, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar)--{"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008820060002108221, 'start': 1685951407.418914, 'stop': 1685951407.419798, '$report_type': 'TestReport', 'item_index': 112, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]"), 'keywords': {"test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0033771449998312164, 'start': 1685951407.4181912, 'stop': 1685951407.421571, '$report_type': 'TestReport', 'item_index': 127, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar)--{"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.003966120000768569, 'start': 1685951407.420476, 'stop': 1685951407.424447, '$report_type': 'TestReport', 'item_index': 112, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +ish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type5-sink_type5-None-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type5-sink_type5-None-None-exception]'), 'keywords': {'test_typechecking[src_type5-sink_type5-None-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type5-sink_type5-None-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018181539999204688, 'start': 1685951407.407179, 'stop': 1685951407.4090009, '$report_type': 'TestReport', 'item_index': 228, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type5-sink_type5-None-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type5-sink_type5-None-None-exception]'), 'keywords': {'test_typechecking[src_type5-sink_type5-None-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type5-sink_type5-None-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005446520008263178, 'start': 1685951407.409743, 'stop': 1685951407.4102888, '$report_type': 'TestReport', 'item_index': 228, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst['lengthz'])] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(lst['lengthz'])]") + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]'), 'keywords': {'test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012807740004063817, 'start': 1685951407.408213, 'stop': 1685951407.4094982, '$report_type': 'TestReport', 'item_index': 126, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavi pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]"), 'keywords': {"test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005704989998776, 'start': 1685951407.422394, 'stop': 1685951407.4229681, '$report_type': 'TestReport', 'item_index': 127, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar)--{"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0009391500007041031, 'start': 1685951407.426031, 'stop': 1685951407.426975, '$report_type': 'TestReport', 'item_index': 112, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type7-sink_type7-merge_nested-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type7-sink_type7-merge_nested-None-pass]'), 'keywords': {'test_typechecking[src_type7-sink_type7-merge_nested-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type7-sink_type7-merge_nested-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0008197139995900216, 'start': 1685951407.4220319, 'stop': 1685951407.422855, '$report_type': 'TestReport', 'item_index': 230, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-\\\\$foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001387401999636495, 'start': 1685951407.423153, 'stop': 1685951407.424543, '$report_type': 'TestReport', 'item_index': 148, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-\\\\$foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0037383649996627355, 'start': 1685951407.425735, 'stop': 1685951407.4294772, '$report_type': 'TestReport', 'item_index': 148, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]'), 'keywords': {'test_parameter_to_expression[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015379240003312589, 'start': 1685951407.425306, 'stop': 1685951407.426848, '$report_type': 'TestReport', 'item_index': 128, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type8-sink_type8-merge_nested-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type8-sink_type8-merge_nested-None-warning]'), 'keywords': {'test_typechecking[src_type8-sink_type8-merge_nested-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type8-sink_type8-merge_nested-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001929928000208747, 'start': 1685951407.425177, 'stop': 1685951407.42711, '$report_type': 'TestReport', 'item_index': 231, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type8-sink_type8-merge_nested-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type8-sink_type8-merge_nested-None-warning]'), 'keywords': {'test_typechecking[src_type8-sink_type8-merge_nested-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type8-sink_type8-merge_nested-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006946809999135439, 'start': 1685951407.4278111, 'stop': 1685951407.4285078, '$report_type': 'TestReport', 'item_index': 231, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type8-sink_type8-merge_nested-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type8-sink_type8-merge_nested-None-warning]'), 'keywords': {'test_typechecking[src_type8-sink_type8-merge_nested-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type8-sink_type8-merge_nested-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007558620000054361, 'start': 1685951407.429294, 'stop': 1685951407.430054, '$report_type': 'TestReport', 'item_index': 231, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]'), 'keywords': {'test_parameter_to_expression[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.003874171999996179, 'start': 1685951407.427493, 'stop': 1685951407.431369, '$report_type': 'TestReport', 'item_index': 128, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-\\\\$foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007411729993691551, 'start': 1685951407.430538, 'stop': 1685951407.4312818, '$report_type': 'TestReport', 'item_index': 148, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]'), 'keywords': {'test_parameter_to_expression[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007541979994130088, 'start': 1685951407.432123, 'stop': 1685951407.4328802, '$report_type': 'TestReport', 'item_index': 128, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]"), 'keywords': {"test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008408759995290893, 'start': 1685951407.4346151, 'stop': 1685951407.435458, '$report_type': 'TestReport', 'item_index': 129, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'bar\'])--{"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'bar\'])--{"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'bar\'])--{"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\'])--{"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.003771616000449285, 'start': 1685951407.4302971, 'stop': 1685951407.43407, '$report_type': 'TestReport', 'item_index': 113, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type9-sink_type9-merge_nested-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type9-sink_type9-merge_nested-None-exception]'), 'keywords': {'test_typechecking[src_type9-sink_type9-merge_nested-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type9-sink_type9-merge_nested-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014442490000874386, 'start': 1685951407.4316878, 'stop': 1685951407.4331362, '$report_type': 'TestReport', 'item_index': 232, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-\\\\foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0010685690003811033, 'start': 1685951407.433168, 'stop': 1685951407.43424, '$report_type': 'TestReport', 'item_index': 149, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +est_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005191010004637064, 'start': 1685951407.401671, 'stop': 1685951407.4021912, '$report_type': 'TestReport', 'item_index': 145, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type4-sink_type4-None-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type4-sink_type4-None-None-warning]'), 'keywords': {'test_typechecking[src_type4-sink_type4-None-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type4-sink_type4-None-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009563419998812606, 'start': 1685951407.40286, 'stop': 1685951407.403818, '$report_type': 'TestReport', 'item_index': 227, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type4-sink_type4-None-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type4-sink_type4-None-None-warning]'), 'keywords': {'test_typechecking[src_type4-sink_type4-None-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type4-sink_type4-None-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004525889999058563, 'start': 1685951407.404313, 'stop': 1685951407.404767, '$report_type': 'TestReport', 'item_index': 227, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nod pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'bar\'])--{"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'bar\'])--{"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'bar\'])--{"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\'])--{"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00048796400005812757, 'start': 1685951407.434898, 'stop': 1685951407.4353878, '$report_type': 'TestReport', 'item_index': 113, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type9-sink_type9-merge_nested-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type9-sink_type9-merge_nested-None-exception]'), 'keywords': {'test_typechecking[src_type9-sink_type9-merge_nested-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type9-sink_type9-merge_nested-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006220549994395697, 'start': 1685951407.4338639, 'stop': 1685951407.434488, '$report_type': 'TestReport', 'item_index': 232, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]"), 'keywords': {"test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.003308045999801834, 'start': 1685951407.436058, 'stop': 1685951407.439368, '$report_type': 'TestReport', 'item_index': 129, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]"), 'keywords': {"test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007918029996289988, 'start': 1685951407.440076, 'stop': 1685951407.440871, '$report_type': 'TestReport', 'item_index': 129, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type9-sink_type9-merge_nested-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type9-sink_type9-merge_nested-None-exception]'), 'keywords': {'test_typechecking[src_type9-sink_type9-merge_nested-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type9-sink_type9-merge_nested-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007315679995372193, 'start': 1685951407.4353259, 'stop': 1685951407.43606, '$report_type': 'TestReport', 'item_index': 232, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-\\\\foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0030199410002751392, 'start': 1685951407.434927, 'stop': 1685951407.43795, '$report_type': 'TestReport', 'item_index': 149, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-\\\\foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005284230001052492, 'start': 1685951407.4385989, 'stop': 1685951407.439129, '$report_type': 'TestReport', 'item_index': 149, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_dedupe', 'location': ('tests/test_examples.py', 576, 'test_dedupe'), 'keywords': {'test_dedupe': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00039291800021601375, 'start': 1685951407.438884, 'stop': 1685951407.439279, '$report_type': 'TestReport', 'item_index': 211, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo.barz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.barz)]') + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["bar"])--{"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001014856000438158, 'start': 1685951407.436694, 'stop': 1685951407.437713, '$report_type': 'TestReport', 'item_index': 114, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_dedupe', 'location': ('tests/test_examples.py', 576, 'test_dedupe'), 'keywords': {'test_dedupe': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0007009029995970195, 'start': 1685951407.439899, 'stop': 1685951407.440602, '$report_type': 'TestReport', 'item_index': 211, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type10-Any-merge_nested-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type10-Any-merge_nested-None-pass]'), 'keywords': {'test_typechecking[src_type10-Any-merge_nested-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type10-Any-merge_nested-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001373458000671235, 'start': 1685951407.4377432, 'stop': 1685951407.439119, '$report_type': 'TestReport', 'item_index': 233, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["bar"])--{"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.004445026000212238, 'start': 1685951407.43843, 'stop': 1685951407.442878, '$report_type': 'TestReport', 'item_index': 114, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_dedupe', 'location': ('tests/test_examples.py', 576, 'test_dedupe'), 'keywords': {'test_dedupe': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0009223950000887271, 'start': 1685951407.44148, 'stop': 1685951407.4424078, '$report_type': 'TestReport', 'item_index': 211, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type10-Any-merge_nested-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type10-Any-merge_nested-None-pass]'), 'keywords': {'test_typechecking[src_type10-Any-merge_nested-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type10-Any-merge_nested-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006485630001407117, 'start': 1685951407.439878, 'stop': 1685951407.4405289, '$report_type': 'TestReport', 'item_index': 233, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$foo-$foo-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["bar"])--{"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004895369993391796, 'start': 1685951407.4440808, 'stop': 1685951407.444572, '$report_type': 'TestReport', 'item_index': 114, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\x-\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006022039997333195, 'start': 1685951407.447602, 'stop': 1685951407.4482071, '$report_type': 'TestReport', 'item_index': 150, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]"), 'keywords': {"test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009072579996427521, 'start': 1685951407.44374, 'stop': 1685951407.444653, '$report_type': 'TestReport', 'item_index': 130, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[0-source0-sink0-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[0-source0-sink0-True]'), 'keywords': {'test_compare_types[0-source0-sink0-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0-source0-sink0-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011165440000695526, 'start': 1685951407.444523, 'stop': 1685951407.445641, '$report_type': 'TestReport', 'item_index': 212, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[0-source0-sink0-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[0-source0-sink0-True]'), 'keywords': {'test_compare_types[0-source0-sink0-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0-source0-sink0-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005950490003669984, 'start': 1685951407.446621, 'stop': 1685951407.447218, '$report_type': 'TestReport', 'item_index': 212, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} +zz"])]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\'ar'].bazz)] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['bar']["bazz"])] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\'ar"].bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] +Höãy`1V°V£4§Äf£ÊÊËp6M`4§i finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo.bar.baz)--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar.baz)--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo.bar.baz)--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.baz)--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000905028000488528, 'start': 1685951407.446458, 'stop': 1685951407.447365, '$report_type': 'TestReport', 'item_index': 115, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]"), 'keywords': {"test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0034936399997604894, 'start': 1685951407.445459, 'stop': 1685951407.4489548, '$report_type': 'TestReport', 'item_index': 130, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]"), 'keywords': {"test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0008037950001380523, 'start': 1685951407.4498649, 'stop': 1685951407.4506721, '$report_type': 'TestReport', 'item_index': 130, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo.bar.baz)--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar.baz)--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo.bar.baz)--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.baz)--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.004031694999866886, 'start': 1685951407.447961, 'stop': 1685951407.451995, '$report_type': 'TestReport', 'item_index': 115, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\foo-foo-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-foo-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo.bar.baz)--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar.baz)--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo.bar.baz)--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.baz)--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004981169995517121, 'start': 1685951407.452596, 'stop': 1685951407.453096, '$report_type': 'TestReport', 'item_index': 115, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[0-source0-sink0-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[0-source0-sink0-True]'), 'keywords': {'test_compare_types[0-source0-sink0-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0-source0-sink0-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006591270002900274, 'start': 1685951407.447834, 'stop': 1685951407.4484951, '$report_type': 'TestReport', 'item_index': 212, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]"), 'keywords': {"test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006833550005467259, 'start': 1685951407.452372, 'stop': 1685951407.453058, '$report_type': 'TestReport', 'item_index': 131, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]"), 'keywords': {"test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.003906683000423072, 'start': 1685951407.453822, 'stop': 1685951407.457731, '$report_type': 'TestReport', 'item_index': 131, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]"), 'keywords': {"test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005058510005255812, 'start': 1685951407.4585779, 'stop': 1685951407.4590871, '$report_type': 'TestReport', 'item_index': 131, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type11-sink_type11-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type11-sink_type11-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type11-sink_type11-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type11-sink_type11-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006146719997559558, 'start': 1685951407.446892, 'stop': 1685951407.447509, '$report_type': 'TestReport', 'item_index': 234, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[1-source1-sink1-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[1-source1-sink1-True]'), 'keywords': {'test_compare_types[1-source1-sink1-True]': 1, 'parametrize': 1, 'pytestmark': 1, '1-source1-sink1-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014154579994283267, 'start': 1685951407.4499588, 'stop': 1685951407.451377, '$report_type': 'TestReport', 'item_index': 213, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[1-source1-sink1-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[1-source1-sink1-True]'), 'keywords': {'test_compare_types[1-source1-sink1-True]': 1, 'parametrize': 1, 'pytestmark': 1, '1-source1-sink1-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004159869995419285, 'start': 1685951407.451968, 'stop': 1685951407.4523861, '$report_type': 'TestReport', 'item_index': 213, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type11-sink_type11-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type11-sink_type11-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type11-sink_type11-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type11-sink_type11-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006853909999335883, 'start': 1685951407.44827, 'stop': 1685951407.448958, '$report_type': 'TestReport', 'item_index': 234, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} +utcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]"), 'keywords': {"test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006833550005467259, 'start': 1685951407.452372, 'stop': 1685951407.453058, '$report_type': 'TestReport', 'item_index': 131, 'worker_id' finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[1-source1-sink1-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[1-source1-sink1-True]'), 'keywords': {'test_compare_types[1-source1-sink1-True]': 1, 'parametrize': 1, 'pytestmark': 1, '1-source1-sink1-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006103440000515548, 'start': 1685951407.452963, 'stop': 1685951407.453575, '$report_type': 'TestReport', 'item_index': 213, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]'), 'keywords': {'test_parameter_to_expression[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00469553899984021, 'start': 1685951407.461876, 'stop': 1685951407.4665742, '$report_type': 'TestReport', 'item_index': 132, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +p': 1685951407.298988, '$report_type': 'TestReport', 'item_index': 184, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type2-sink_type2-None-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type2-sink_type2-None-None-exception]'), 'keywords': {'test_typechecking[src_type2-sink_type2-None-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type2-sink_type2-None-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007488389992431621, 'start': 1685951407.395227, 'stop': 1685951407.3959758, '$report_type': 'TestReport', 'item_index': 225, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type2-sink_type2-None-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type2-sink_type2-None-None-exception]'), 'keywords': {'test_typechecking[src_type2-sink_type2-None-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type2-sink_type2-None-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00038672000027872855, 'start': 1685951407.3965921, 'stop': 1685951407.39698, '$report_type': 'TestReport', 'item_index': 225, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type2-sink_type2-None-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type2-sink_type2-None-None-exception]'), 'keywords': {'test_typechecking[src_type2-sink_type2-None-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type2-sink_type2-None-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00036709400046675, 'start': 1685951407.397452, 'stop': 1685951407.39782, '$report_type': 'TestReport', 'item_index': 225, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo['bar'].baz)--zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['bar'].baz)--zab1]"), 'keywords': {"test_parameter_to_expression[-$(foo['bar'].baz)--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].baz)--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008441309992122115, 'start': 1685951407.454777, 'stop': 1685951407.455623, '$report_type': 'TestReport', 'item_index': 116, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo['bar'].baz)--zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['bar'].baz)--zab1]"), 'keywords': {"test_parameter_to_expression[-$(foo['bar'].baz)--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].baz)--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0038422269999500713, 'start': 1685951407.456418, 'stop': 1685951407.460264, '$report_type': 'TestReport', 'item_index': 116, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo.barz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.barz)]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type12-sink_type12-merge_flattened-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type12-sink_type12-merge_flattened-None-warning]'), 'keywords': {'test_typechecking[src_type12-sink_type12-merge_flattened-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type12-sink_type12-merge_flattened-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014149050002743024, 'start': 1685951407.45079, 'stop': 1685951407.452208, '$report_type': 'TestReport', 'item_index': 235, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 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'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\x-\\\\\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0012658139994528028, 'start': 1685951407.463109, 'stop': 1685951407.464381, '$report_type': 'TestReport', 'item_index': 152, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type12-sink_type12-merge_flattened-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type12-sink_type12-merge_flattened-None-warning]'), 'keywords': {'test_typechecking[src_type12-sink_type12-merge_flattened-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type12-sink_type12-merge_flattened-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005353910000849282, 'start': 1685951407.4543848, 'stop': 1685951407.454922, '$report_type': 'TestReport', 'item_index': 235, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo['bar'].baz)--zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['bar'].baz)--zab1]"), 'keywords': {"test_parameter_to_expression[-$(foo['bar'].baz)--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].baz)--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006598230002055061, 'start': 1685951407.461045, 'stop': 1685951407.461707, '$report_type': 'TestReport', 'item_index': 116, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[2-source2-sink2-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[2-source2-sink2-True]'), 'keywords': {'test_compare_types[2-source2-sink2-True]': 1, 'parametrize': 1, 'pytestmark': 1, '2-source2-sink2-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013290569995660917, 'start': 1685951407.455175, 'stop': 1685951407.456508, '$report_type': 'TestReport', 'item_index': 214, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[2-source2-sink2-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[2-source2-sink2-True]'), 'keywords': {'test_compare_types[2-source2-sink2-True]': 1, 'parametrize': 1, 'pytestmark': 1, '2-source2-sink2-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005690930001946981, 'start': 1685951407.457442, 'stop': 1685951407.458014, '$report_type': 'TestReport', 'item_index': 214, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['barz'])] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['barz'])]") + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[2-source2-sink2-True]', 'location': 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'keywords': {'test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008231579995481297, 'start': 1685951407.4694579, 'stop': 1685951407.470283, '$report_type': 'TestReport', 'item_index': 133, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]'), 'keywords': {'test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00349459700009902, 'start': 1685951407.4709928, 'stop': 1685951407.4744902, '$report_type': 'TestReport', 'item_index': 133, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007233100004668813, 'start': 1685951407.466839, 'stop': 1685951407.467564, '$report_type': 'TestReport', 'item_index': 153, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': 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'test_compare_types[3-source3-sink3-False]'), 'keywords': {'test_compare_types[3-source3-sink3-False]': 1, 'parametrize': 1, 'pytestmark': 1, '3-source3-sink3-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0012149430003773887, 'start': 1685951407.462949, 'stop': 1685951407.4641678, '$report_type': 'TestReport', 'item_index': 215, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["baz"])--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015898760002528434, 'start': 1685951407.46432, 'stop': 1685951407.465913, '$report_type': 'TestReport', 'item_index': 117, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\x-x-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\x-x-1]') + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007493510001950199, 'start': 1685951407.471963, 'stop': 1685951407.472715, '$report_type': 'TestReport', 'item_index': 153, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]'), 'keywords': {'test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005360660006772378, 'start': 1685951407.475329, 'stop': 1685951407.4758668, '$report_type': 'TestReport', 'item_index': 133, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["baz"])--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00325770199924591, 'start': 1685951407.466681, 'stop': 1685951407.469941, '$report_type': 'TestReport', 'item_index': 117, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["baz"])--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006352569998853141, 'start': 1685951407.470835, 'stop': 1685951407.471473, '$report_type': 'TestReport', 'item_index': 117, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type13-sink_type13-merge_flattened-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type13-sink_type13-merge_flattened-None-exception]'), 'keywords': {'test_typechecking[src_type13-sink_type13-merge_flattened-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type13-sink_type13-merge_flattened-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00045605000013893005, 'start': 1685951407.45876, 'stop': 1685951407.45922, '$report_type': 'TestReport', 'item_index': 236, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type13-sink_type13-merge_flattened-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type13-sink_type13-merge_flattened-None-exception]'), 'keywords': {'test_typechecking[src_type13-sink_type13-merge_flattened-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type13-sink_type13-merge_flattened-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005032700000811019, 'start': 1685951407.45975, 'stop': 1685951407.460256, '$report_type': 'TestReport', 'item_index': 236, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[3-source3-sink3-False]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[3-source3-sink3-False]'), 'keywords': {'test_compare_types[3-source3-sink3-False]': 1, 'parametrize': 1, 'pytestmark': 1, '3-source3-sink3-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0009851459999481449, 'start': 1685951407.465446, 'stop': 1685951407.466434, '$report_type': 'TestReport', 'item_index': 215, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(fooz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(fooz)]'), 'keywords': {'test_expression_interpolate_failures[$(fooz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(fooz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006368700005623396, 'start': 1685951407.474289, 'stop': 1685951407.4749281, '$report_type': 'TestReport', 'item_index': 154, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(fooz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(fooz)]'), 'keywords': {'test_expression_interpolate_failures[$(fooz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(fooz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0008318189993588021, 'start': 1685951407.475588, 'stop': 1685951407.4764218, '$report_type': 'TestReport', 'item_index': 154, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013473919998432393, 'start': 1685951407.477623, 'stop': 1685951407.4789739, '$report_type': 'TestReport', 'item_index': 134, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0028304689994911314, 'start': 1685951407.479712, 'stop': 1685951407.482545, '$report_type': 'TestReport', 'item_index': 134, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo.bar['baz'])--zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo.bar['baz'])--zab1]"), 'keywords': {"test_parameter_to_expression[-$(foo.bar['baz'])--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['baz'])--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006902869999976247, 'start': 1685951407.473063, 'stop': 1685951407.473755, '$report_type': 'TestReport', 'item_index': 118, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo.bar['baz'])--zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo.bar['baz'])--zab1]"), 'keywords': {"test_parameter_to_expression[-$(foo.bar['baz'])--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['baz'])--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0036005160000058822, 'start': 1685951407.47429, 'stop': 1685951407.477893, '$report_type': 'TestReport', 'item_index': 118, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo.bar['baz'])--zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo.bar['baz'])--zab1]"), 'keywords': {"test_parameter_to_expression[-$(foo.bar['baz'])--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['baz'])--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005814630003442289, 'start': 1685951407.47889, 'stop': 1685951407.4794738, '$report_type': 'TestReport', 'item_index': 118, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0011832519994641189, 'start': 1685951407.483479, 'stop': 1685951407.484666, '$report_type': 'TestReport', 'item_index': 134, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(fooz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(fooz)]'), 'keywords': {'test_expression_interpolate_failures[$(fooz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(fooz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007369049999397248, 'start': 1685951407.477133, 'stop': 1685951407.4778728, '$report_type': 'TestReport', 'item_index': 154, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[record 0-source4-sink4-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[record 0-source4-sink4-True]'), 'keywords': {'test_compare_types[record 0-source4-sink4-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'record 0-source4-sink4-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008855000005496549, 'start': 1685951407.46778, 'stop': 1685951407.4686668, '$report_type': 'TestReport', 'item_index': 216, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type14-sink_type14-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type14-sink_type14-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type14-sink_type14-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type14-sink_type14-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015560199999526958, 'start': 1685951407.4616451, 'stop': 1685951407.4632058, '$report_type': 'TestReport', 'item_index': 237, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type14-sink_type14-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type14-sink_type14-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type14-sink_type14-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type14-sink_type14-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0014577689998986898, 'start': 1685951407.464467, 'stop': 1685951407.4659278, '$report_type': 'TestReport', 'item_index': 237, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[record 0-source4-sink4-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[record 0-source4-sink4-True]'), 'keywords': {'test_compare_types[record 0-source4-sink4-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'record 0-source4-sink4-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000649294999675476, 'start': 1685951407.469322, 'stop': 1685951407.469973, '$report_type': 'TestReport', 'item_index': 216, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[record 0-source4-sink4-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[record 0-source4-sink4-True]'), 'keywords': {'test_compare_types[record 0-source4-sink4-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'record 0-source4-sink4-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007126489999791374, 'start': 1685951407.470677, 'stop': 1685951407.471393, '$report_type': 'TestReport', 'item_index': 216, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.barz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo.barz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo.barz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.barz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006304079997789813, 'start': 1685951407.4798121, 'stop': 1685951407.480444, '$report_type': 'TestReport', 'item_index': 155, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000916687999961141, 'start': 1685951407.487365, 'stop': 1685951407.4882839, '$report_type': 'TestReport', 'item_index': 135, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo['b ar'].baz)--2]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['b ar'].baz)--2]"), 'keywords': {"test_parameter_to_expression[-$(foo['b ar'].baz)--2]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b ar'].baz)--2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006417999993573176, 'start': 1685951407.4810822, 'stop': 1685951407.481726, '$report_type': 'TestReport', 'item_index': 119, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo['b ar'].baz)--2]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['b ar'].baz)--2]"), 'keywords': {"test_parameter_to_expression[-$(foo['b ar'].baz)--2]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b ar'].baz)--2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.004785899000125937, 'start': 1685951407.482217, 'stop': 1685951407.487005, '$report_type': 'TestReport', 'item_index': 119, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.barz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo.barz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo.barz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.barz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005517300005521975, 'start': 1685951407.4811351, 'stop': 1685951407.481688, '$report_type': 'TestReport', 'item_index': 155, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: +erpolate_failures[-$(foo['barz'])]" when='teardown' outcome='passed'> [hook] + [hook] + pytest_report_from_serializable ÚÚ<_pytest.config.Config object at 0x11074ef80> + ¬/test_examples.py::test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]"), 'keywords': {"test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]": 1, 'parametrize': 1, 'pyt pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[record 1-source5-sink5-False]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[record 1-source5-sink5-False]'), 'keywords': {'test_compare_types[record 1-source5-sink5-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'record 1-source5-sink5-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005380510001486982, 'start': 1685951407.4761322, 'stop': 1685951407.476672, '$report_type': 'TestReport', 'item_index': 217, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0031796220000614994, 'start': 1685951407.48895, 'stop': 1685951407.4921322, '$report_type': 'TestReport', 'item_index': 135, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo['b ar'].baz)--2]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['b ar'].baz)--2]"), 'keywords': {"test_parameter_to_expression[-$(foo['b ar'].baz)--2]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b ar'].baz)--2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004766259999087197, 'start': 1685951407.487801, 'stop': 1685951407.48828, '$report_type': 'TestReport', 'item_index': 119, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +ter_to_expression[-$(foo['bar'].baz)--zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['bar'].baz)--zab1]"), 'keywords': {"test_parameter_to_expression[-$(foo['bar'].baz)--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].baz)--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006598230002055061, 'start': 1685951407.461045, 'stop': 1685951407.461707, '$report_type': 'TestReport', 'item_index': 116, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[2-source2-sink2-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[2-source2-sink2-True]'), 'keywords': {'test_compare_types[2-source2-sink2-True]': 1, 'parametrize': 1, 'pytestmark': 1, '2-source2-sink2-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013290569995660917, 'start': 1685951407.455175, 'stop': 1685951407.456508, '$report_type': 'TestReport', 'item_index': 214, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[2-source2-sink2-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[2-source2-sink2-True]'), 'keywords': {'test_compare_types[2-source2-sink2-True]': 1, 'parametrize': 1, 'pytestmark': 1, '2-source2-sink2-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005690930001946981, 'start': 1685951407.457442, 'stop': 1685951407.458014, '$report_type': 'TestReport', 'item_index': 214, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['barz'])] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['barz'])]") + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types[2-source2-sink2-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[2-source2-sink2-True]'), 'keywords': {'test_compare_types[2-source2-sink2-True]': 1, 'parametrize': 1, 'pytestmark': 1, '2-source2-sink2-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000625794999905338, 'start': 1685951407.45877, 'stop': 1685951407.459397, '$report_type': 'TestReport', 'item_index': 214, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +ssed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002835494999999355, 'start': 1685 pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo['barz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['barz'])]"), 'keywords': {"test_expression_interpolate_failures[$(foo['barz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['barz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013087470006212243, 'start': 1685951407.485544, 'stop': 1685951407.486857, '$report_type': 'TestReport', 'item_index': 156, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011623079999480979, 'start': 1685951407.49646, 'stop': 1685951407.497626, '$report_type': 'TestReport', 'item_index': 136, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002443803999994998, 'start': 1685951407.4981608, 'stop': 1685951407.500606, '$report_type': 'TestReport', 'item_index': 136, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005341539999790257, 'start': 1685951407.501076, 'stop': 1685951407.501611, '$report_type': 'TestReport', 'item_index': 136, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007855650001147296, 'start': 1685951407.489816, 'stop': 1685951407.490603, '$report_type': 'TestReport', 'item_index': 193, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +74ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type10-Any-merge_nested-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type10-Any-merge_nested-None-pass]'), 'keywords': {'test_typechecking[src_type10-Any-merge_nested-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type10-Any-merge_nested-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006485630001407117, 'start': 1685951407.439878, 'stop': 1685951407.4405289, '$report_type': 'TestReport', 'item_index': 233, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$foo-$foo-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-$foo pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[0-source0-sink0-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[0-source0-sink0-True]'), 'keywords': {'test_compare_types_strict[0-source0-sink0-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0-source0-sink0-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012504549995355774, 'start': 1685951407.4789708, 'stop': 1685951407.480224, '$report_type': 'TestReport', 'item_index': 218, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007740010005363729, 'start': 1685951407.492597, 'stop': 1685951407.493373, '$report_type': 'TestReport', 'item_index': 193, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo["barz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo["barz"])]'), 'keywords': {'test_expression_interpolate_failures[$(foo["barz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["barz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005903749997742125, 'start': 1685951407.491008, 'stop': 1685951407.4915998, '$report_type': 'TestReport', 'item_index': 157, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +ion': 0.0012149430003773887, 'start': 1685951407.462949, 'stop': 1685951407.4641678, '$report_type': 'TestReport', 'item_index': 215, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["baz"])--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015898760002528434, 'start': 1685951407.46432, 'stop': 1685951407.465913, '$report_type': 'TestReport', 'item_index': 117, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\x-x-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\x-x-1]') + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007493510001950199, 'start': 1685951407.471963, 'stop': 1685951407.472715, '$report_type': 'TestReport', 'item_index': 153, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]'), 'keywords': {'test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005360660006772378, 'start': 1685951407.475329, 'stop': 1685951407.4758668, '$report_type': 'TestReport', 'item_index': 133, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]': 1, 'parametrize': 1, 'pytestm pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-\\\\$foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015040170001157094, 'start': 1685951407.4960089, 'stop': 1685951407.497517, '$report_type': 'TestReport', 'item_index': 194, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012119149996578926, 'start': 1685951407.502867, 'stop': 1685951407.504081, '$report_type': 'TestReport', 'item_index': 137, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[0-source0-sink0-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[0-source0-sink0-True]'), 'keywords': {'test_compare_types_strict[0-source0-sink0-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0-source0-sink0-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005703129991161404, 'start': 1685951407.480953, 'stop': 1685951407.481526, '$report_type': 'TestReport', 'item_index': 218, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-\\\\$foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003057240000998718, 'start': 1685951407.498126, 'stop': 1685951407.498433, '$report_type': 'TestReport', 'item_index': 194, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo["barz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo["barz"])]'), 'keywords': {'test_expression_interpolate_failures[$(foo["barz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["barz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00044038600026397035, 'start': 1685951407.4921641, 'stop': 1685951407.492606, '$report_type': 'TestReport', 'item_index': 157, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar.bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo.bar.bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo.bar.bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001430157999493531, 'start': 1685951407.495042, 'stop': 1685951407.496477, '$report_type': 'TestReport', 'item_index': 158, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar.bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo.bar.bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo.bar.bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00046733999988646246, 'start': 1685951407.497409, 'stop': 1685951407.497877, '$report_type': 'TestReport', 'item_index': 158, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-\\\\$foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005012780002289219, 'start': 1685951407.498927, 'stop': 1685951407.49943, '$report_type': 'TestReport', 'item_index': 194, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\x-\\x-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['barz'])] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['barz'])]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[0-source0-sink0-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[0-source0-sink0-True]'), 'keywords': {'test_compare_types_strict[0-source0-sink0-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0-source0-sink0-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005009080005038413, 'start': 1685951407.482143, 'stop': 1685951407.482645, '$report_type': 'TestReport', 'item_index': 218, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002640106999933778, 'start': 1685951407.504642, 'stop': 1685951407.507284, '$report_type': 'TestReport', 'item_index': 137, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000696269000400207, 'start': 1685951407.50822, 'stop': 1685951407.508919, '$report_type': 'TestReport', 'item_index': 137, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-$foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008419430005233153, 'start': 1685951407.510935, 'stop': 1685951407.511779, '$report_type': 'TestReport', 'item_index': 138, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar.bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo.bar.bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo.bar.bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004244880001351703, 'start': 1685951407.498385, 'stop': 1685951407.4988108, '$report_type': 'TestReport', 'item_index': 158, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-\\\\foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005957029998171492, 'start': 1685951407.5008461, 'stop': 1685951407.5014431, '$report_type': 'TestReport', 'item_index': 195, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-\\\\foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004010249995189952, 'start': 1685951407.501905, 'stop': 1685951407.5023072, '$report_type': 'TestReport', 'item_index': 195, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-\\\\foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005769700001110323, 'start': 1685951407.502945, 'stop': 1685951407.503524, '$report_type': 'TestReport', 'item_index': 195, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[1-source1-sink1-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[1-source1-sink1-True]'), 'keywords': {'test_compare_types_strict[1-source1-sink1-True]': 1, 'parametrize': 1, 'pytestmark': 1, '1-source1-sink1-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0021377479997681803, 'start': 1685951407.484278, 'stop': 1685951407.486421, '$report_type': 'TestReport', 'item_index': 219, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[1-source1-sink1-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[1-source1-sink1-True]'), 'keywords': {'test_compare_types_strict[1-source1-sink1-True]': 1, 'parametrize': 1, 'pytestmark': 1, '1-source1-sink1-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005397120003181044, 'start': 1685951407.487469, 'stop': 1685951407.4880111, '$report_type': 'TestReport', 'item_index': 219, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[1-source1-sink1-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[1-source1-sink1-True]'), 'keywords': {'test_compare_types_strict[1-source1-sink1-True]': 1, 'parametrize': 1, 'pytestmark': 1, '1-source1-sink1-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006269000004976988, 'start': 1685951407.488662, 'stop': 1685951407.489291, '$report_type': 'TestReport', 'item_index': 219, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[2-source2-sink2-False]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[2-source2-sink2-False]'), 'keywords': {'test_compare_types_strict[2-source2-sink2-False]': 1, 'parametrize': 1, 'pytestmark': 1, '2-source2-sink2-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0010110920002261992, 'start': 1685951407.490805, 'stop': 1685951407.491818, '$report_type': 'TestReport', 'item_index': 220, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-$foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002260958000078972, 'start': 1685951407.512245, 'stop': 1685951407.514508, '$report_type': 'TestReport', 'item_index': 138, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-$foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003451669999776641, 'start': 1685951407.515003, 'stop': 1685951407.515349, '$report_type': 'TestReport', 'item_index': 138, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\x-\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006175739999889629, 'start': 1685951407.504673, 'stop': 1685951407.505292, '$report_type': 'TestReport', 'item_index': 196, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo["barz"])] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["barz"])]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\x-\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002839520002453355, 'start': 1685951407.505698, 'stop': 1685951407.505984, '$report_type': 'TestReport', 'item_index': 196, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[3-source3-sink3-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[3-source3-sink3-True]'), 'keywords': {'test_compare_types_strict[3-source3-sink3-True]': 1, 'parametrize': 1, 'pytestmark': 1, '3-source3-sink3-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012008260000584414, 'start': 1685951407.496809, 'stop': 1685951407.4980118, '$report_type': 'TestReport', 'item_index': 221, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[3-source3-sink3-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[3-source3-sink3-True]'), 'keywords': {'test_compare_types_strict[3-source3-sink3-True]': 1, 'parametrize': 1, 'pytestmark': 1, '3-source3-sink3-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00039560899949719897, 'start': 1685951407.498655, 'stop': 1685951407.499052, '$report_type': 'TestReport', 'item_index': 221, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[3-source3-sink3-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[3-source3-sink3-True]'), 'keywords': {'test_compare_types_strict[3-source3-sink3-True]': 1, 'parametrize': 1, 'pytestmark': 1, '3-source3-sink3-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004933200007144478, 'start': 1685951407.499584, 'stop': 1685951407.5000792, '$report_type': 'TestReport', 'item_index': 221, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] +ord 0-source4-sink4-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[record 0-source4-sink4-True]'), 'keywords': {'test_compare_types[record 0-source4-sink4-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'record 0-source4-sink4-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007126489999791374, 'start': 1685951407.470677, 'stop': 1685951407.471393, '$report_type': 'TestReport', 'item_index': 216, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.barz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo.barz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo.barz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.barz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006304079997789813, 'start': 1685951407.4798121, 'stop': 1685951407.480444, '$report_type': 'TestReport', 'item_index': 155, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 't pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[4-source4-sink4-False]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[4-source4-sink4-False]'), 'keywords': {'test_compare_types_strict[4-source4-sink4-False]': 1, 'parametrize': 1, 'pytestmark': 1, '4-source4-sink4-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000619779000771814, 'start': 1685951407.501056, 'stop': 1685951407.501677, '$report_type': 'TestReport', 'item_index': 222, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\x-\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00034795000010490185, 'start': 1685951407.506422, 'stop': 1685951407.5067708, '$report_type': 'TestReport', 'item_index': 196, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[4-source4-sink4-False]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[4-source4-sink4-False]'), 'keywords': {'test_compare_types_strict[4-source4-sink4-False]': 1, 'parametrize': 1, 'pytestmark': 1, '4-source4-sink4-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004853569998886087, 'start': 1685951407.502296, 'stop': 1685951407.502783, '$report_type': 'TestReport', 'item_index': 222, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[4-source4-sink4-False]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[4-source4-sink4-False]'), 'keywords': {'test_compare_types_strict[4-source4-sink4-False]': 1, 'parametrize': 1, 'pytestmark': 1, '4-source4-sink4-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007194259997049812, 'start': 1685951407.503436, 'stop': 1685951407.504158, '$report_type': 'TestReport', 'item_index': 222, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009104320006372291, 'start': 1685951407.508001, 'stop': 1685951407.508914, '$report_type': 'TestReport', 'item_index': 197, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0007237869995151414, 'start': 1685951407.509758, 'stop': 1685951407.510485, '$report_type': 'TestReport', 'item_index': 197, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004891950002274825, 'start': 1685951407.5112882, 'stop': 1685951407.511779, '$report_type': 'TestReport', 'item_index': 197, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo["barz"])] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["barz"])]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\x-\\\\\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007175889995778562, 'start': 1685951407.5128021, 'stop': 1685951407.513521, '$report_type': 'TestReport', 'item_index': 198, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\x-\\\\\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003817039996647509, 'start': 1685951407.514105, 'stop': 1685951407.5144892, '$report_type': 'TestReport', 'item_index': 198, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\x-\\\\\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00039627899968763813, 'start': 1685951407.515075, 'stop': 1685951407.515473, '$report_type': 'TestReport', 'item_index': 198, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0010752340003818972, 'start': 1685951407.516592, 'stop': 1685951407.5176709, '$report_type': 'TestReport', 'item_index': 199, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004985229998055729, 'start': 1685951407.518878, 'stop': 1685951407.519379, '$report_type': 'TestReport', 'item_index': 199, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003379379995749332, 'start': 1685951407.519968, 'stop': 1685951407.5203068, '$report_type': 'TestReport', 'item_index': 199, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar.bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.bar.bazz)]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_factory', 'location': ('tests/test_examples.py', 284, 'test_factory'), 'keywords': {'test_factory': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00022203000025911024, 'start': 1685951407.521238, 'stop': 1685951407.521461, '$report_type': 'TestReport', 'item_index': 200, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\x-\\x-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\x-\\x-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar.bazz)] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.bar.bazz)]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar'].bazz)] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['bar'].bazz)]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\x-\\x-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar'].bazz)] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['bar'].bazz)]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar']["bazz"])] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$(foo.bar.baz)-$(foo.bar.baz)-2] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar']["bazz"])] + location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$(foo.bar.baz)-$(foo.bar.baz)-2] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-\\zab1-2] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar['bazz'])] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo.bar['bazz'])]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-\\zab1-2] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar['bazz'])] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo.bar['bazz'])]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\$(foo.bar.baz)-\\$(foo.bar.baz)-2] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo['b\\'ar'].baz)--true] + location: ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['b\\\\'ar'].baz)--true]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\x-x-1] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo["b\\'ar"].baz)--true] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\$(foo.bar.baz)-\\$(foo.bar.baz)-2] + location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\x-1] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_trick_scandeps + location: ('tests/test_examples.py', 549, 'test_trick_scandeps') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo["b\\'ar"].baz)--true] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\x-1] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo['b\\"ar'].baz)--null] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\x-\\x-1] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b ar'].bazz)] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b ar'].bazz)]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo['b\\"ar'].baz)--null] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\x-\\x-1] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b ar'].bazz)] + location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b ar'].bazz)]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type1-sink_type1-None-None-warning] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type1-sink_type1-None-None-warning]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type1-sink_type1-None-None-warning] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type1-sink_type1-None-None-warning]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type2-sink_type2-None-None-exception] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type2-sink_type2-None-None-exception]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\$(foo.bar.baz)-$(foo.bar.baz)-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type2-sink_type2-None-None-exception] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type2-sink_type2-None-None-exception]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type3-sink_type3-None-None-pass] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type3-sink_type3-None-None-pass]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo['bar']) $(foo['bar'])-{"baz":"zab1"} {"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo['bar']) $(foo['bar'])-{"baz":"zab1"} {"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\$(foo.bar.baz)-$(foo.bar.baz)-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-\\zab1-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type3-sink_type3-None-None-pass] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type3-sink_type3-None-None-pass]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type4-sink_type4-None-None-warning] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type4-sink_type4-None-None-warning]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type15-sink_type15-merge_flattened-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type15-sink_type15-merge_flattened-None-warning]'), 'keywords': {'test_typechecking[src_type15-sink_type15-merge_flattened-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type15-sink_type15-merge_flattened-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000966904000051727, 'start': 1685951407.5596402, 'stop': 1685951407.560609, '$report_type': 'TestReport', 'item_index': 238, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_trick_scandeps + location: ('tests/test_examples.py', 549, 'test_trick_scandeps') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-\\zab1-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_scandeps_defaults_with_secondaryfiles + location: ('tests/test_examples.py', 559, 'test_scandeps_defaults_with_secondaryfiles') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type15-sink_type15-merge_flattened-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type15-sink_type15-merge_flattened-None-warning]'), 'keywords': {'test_typechecking[src_type15-sink_type15-merge_flattened-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type15-sink_type15-merge_flattened-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003950609998355503, 'start': 1685951407.560992, 'stop': 1685951407.561389, '$report_type': 'TestReport', 'item_index': 238, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type15-sink_type15-merge_flattened-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type15-sink_type15-merge_flattened-None-warning]'), 'keywords': {'test_typechecking[src_type15-sink_type15-merge_flattened-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type15-sink_type15-merge_flattened-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00036564799938787473, 'start': 1685951407.5619452, 'stop': 1685951407.562312, '$report_type': 'TestReport', 'item_index': 238, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type16-sink_type16-merge_flattened-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type16-sink_type16-merge_flattened-None-exception]'), 'keywords': {'test_typechecking[src_type16-sink_type16-merge_flattened-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type16-sink_type16-merge_flattened-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006378789994414547, 'start': 1685951407.563191, 'stop': 1685951407.56383, '$report_type': 'TestReport', 'item_index': 239, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type16-sink_type16-merge_flattened-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type16-sink_type16-merge_flattened-None-exception]'), 'keywords': {'test_typechecking[src_type16-sink_type16-merge_flattened-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type16-sink_type16-merge_flattened-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003123340002275654, 'start': 1685951407.564163, 'stop': 1685951407.564476, '$report_type': 'TestReport', 'item_index': 239, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type16-sink_type16-merge_flattened-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type16-sink_type16-merge_flattened-None-exception]'), 'keywords': {'test_typechecking[src_type16-sink_type16-merge_flattened-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type16-sink_type16-merge_flattened-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003279310003563296, 'start': 1685951407.564853, 'stop': 1685951407.565182, '$report_type': 'TestReport', 'item_index': 239, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type4-sink_type4-None-None-warning] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type4-sink_type4-None-None-warning]') + finish pytest_runtest_logfinish --> [] [hook] +es.py::test_expression_interpolate[-$(foo[\'barÚaz": "zÚhen='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config objec pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type5-sink_type5-None-None-exception] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type5-sink_type5-None-None-exception]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type17-Any-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type17-Any-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type17-Any-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type17-Any-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006902300001456751, 'start': 1685951407.565999, 'stop': 1685951407.5666912, '$report_type': 'TestReport', 'item_index': 240, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type17-Any-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type17-Any-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type17-Any-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type17-Any-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003467900005489355, 'start': 1685951407.567265, 'stop': 1685951407.5676138, '$report_type': 'TestReport', 'item_index': 240, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type17-Any-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type17-Any-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type17-Any-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type17-Any-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00046973099961178377, 'start': 1685951407.5681632, 'stop': 1685951407.568634, '$report_type': 'TestReport', 'item_index': 240, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type5-sink_type5-None-None-exception] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type5-sink_type5-None-None-exception]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type6-sink_type6-merge_nested-None-exception] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type6-sink_type6-merge_nested-None-exception]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type18-Any-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type18-Any-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type18-Any-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type18-Any-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009511629996268312, 'start': 1685951407.569459, 'stop': 1685951407.570412, '$report_type': 'TestReport', 'item_index': 241, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\$(foo.bar.baz)-\\$(foo.bar.baz)-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type18-Any-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type18-Any-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type18-Any-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type18-Any-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00023513900032412494, 'start': 1685951407.5708318, 'stop': 1685951407.5710678, '$report_type': 'TestReport', 'item_index': 241, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type18-Any-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type18-Any-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type18-Any-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type18-Any-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00036264399932406377, 'start': 1685951407.571399, 'stop': 1685951407.571763, '$report_type': 'TestReport', 'item_index': 241, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1] + location: ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 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pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type19-sink_type19-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type19-sink_type19-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type19-sink_type19-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type19-sink_type19-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0008626649996585911, 'start': 1685951407.573952, 'stop': 1685951407.574819, '$report_type': 'TestReport', 'item_index': 242, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type19-sink_type19-merge_flattened-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type19-sink_type19-merge_flattened-None-pass]'), 'keywords': {'test_typechecking[src_type19-sink_type19-merge_flattened-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type19-sink_type19-merge_flattened-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004830799998671864, 'start': 1685951407.575933, 'stop': 1685951407.5764182, '$report_type': 'TestReport', 'item_index': 242, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type7-sink_type7-merge_nested-None-pass] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type7-sink_type7-merge_nested-None-pass]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] +eport: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytes finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type20-sink_type20-merge_flattened-special value-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type20-sink_type20-merge_flattened-special value-pass]'), 'keywords': {'test_typechecking[src_type20-sink_type20-merge_flattened-special value-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type20-sink_type20-merge_flattened-special value-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007166690002122778, 'start': 1685951407.577311, 'stop': 1685951407.5780292, '$report_type': 'TestReport', 'item_index': 243, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type20-sink_type20-merge_flattened-special value-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type20-sink_type20-merge_flattened-special value-pass]'), 'keywords': {'test_typechecking[src_type20-sink_type20-merge_flattened-special value-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type20-sink_type20-merge_flattened-special value-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00023158299973147223, 'start': 1685951407.578479, 'stop': 1685951407.578712, '$report_type': 'TestReport', 'item_index': 243, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type20-sink_type20-merge_flattened-special value-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type20-sink_type20-merge_flattened-special value-pass]'), 'keywords': {'test_typechecking[src_type20-sink_type20-merge_flattened-special value-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type20-sink_type20-merge_flattened-special value-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00032688200008124113, 'start': 1685951407.579066, 'stop': 1685951407.579394, '$report_type': 'TestReport', 'item_index': 243, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\$foo-\\$foo-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1] + location: ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['bar'].baz) $(foo['bar'].baz)-zab1 zab1]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type7-sink_type7-merge_nested-None-pass] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type7-sink_type7-merge_nested-None-pass]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo['bar']["baz"]) $(foo['bar']["baz"])-zab1 zab1] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type8-sink_type8-merge_nested-None-warning] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type8-sink_type8-merge_nested-None-warning]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo['bar']["baz"]) $(foo['bar']["baz"])-zab1 zab1] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type8-sink_type8-merge_nested-None-warning] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type8-sink_type8-merge_nested-None-warning]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: +tstatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\x-x-1] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]') + finish pytest_runtest_logfinish --> [] [hook] +::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1] + location: ('tests/test_examples.py', pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1] + location: ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\$foo-\\$foo-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo['bar'])--{"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'bar\'])--{"baz":"zab1"}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type9-sink_type9-merge_nested-None-exception] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type9-sink_type9-merge_nested-None-exception]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-foo-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-foo-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005884160000277916, 'start': 1685951407.58587, 'stop': 1685951407.5864599, '$report_type': 'TestReport', 'item_index': 139, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\foo-\\foo-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo['bar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['bar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[$(foo['bar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005376250001063454, 'start': 1685951407.5870578, 'stop': 1685951407.587598, '$report_type': 'TestReport', 'item_index': 159, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_scandeps_defaults_with_secondaryfiles + location: ('tests/test_examples.py', 559, 'test_scandeps_defaults_with_secondaryfiles') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo['bar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['bar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[$(foo['bar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004152920000706217, 'start': 1685951407.5881479, 'stop': 1685951407.588564, '$report_type': 'TestReport', 'item_index': 159, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-foo-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-foo-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002118020999660075, 'start': 1685951407.586812, 'stop': 1685951407.588931, '$report_type': 'TestReport', 'item_index': 139, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo['bar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['bar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[$(foo['bar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00031103200035431655, 'start': 1685951407.589112, 'stop': 1685951407.5894241, '$report_type': 'TestReport', 'item_index': 159, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-foo-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-foo-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003145649998259614, 'start': 1685951407.589335, 'stop': 1685951407.5896509, '$report_type': 'TestReport', 'item_index': 139, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo['bar'])--{"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'bar\'])--{"baz":"zab1"}]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_var_spool_cwl_checker2', 'location': ('tests/test_examples.py', 960, 'test_var_spool_cwl_checker2'), 'keywords': {'test_var_spool_cwl_checker2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008067179996942286, 'start': 1685951407.591139, 'stop': 1685951407.5919511, '$report_type': 'TestReport', 'item_index': 253, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_dedupe + location: ('tests/test_examples.py', 576, 'test_dedupe') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\foo-\\foo-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type9-sink_type9-merge_nested-None-exception] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type9-sink_type9-merge_nested-None-exception]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_dir[--parallel --debug]', 'location': ('tests/test_examples.py', 1084, 'test_cid_file_dir[--parallel --debug]'), 'keywords': {'test_cid_file_dir[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0035731289999603177, 'start': 1685951407.590938, 'stop': 1685951407.594513, '$report_type': 'TestReport', 'item_index': 267, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type10-Any-merge_nested-None-pass] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type10-Any-merge_nested-None-pass]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1] + location: ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_dedupe + location: ('tests/test_examples.py', 576, 'test_dedupe') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\x-\\x-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2] + location: ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_compare_types[0-source0-sink0-True] + location: ('tests/test_examples.py', 648, 'test_compare_types[0-source0-sink0-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type10-Any-merge_nested-None-pass] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type10-Any-merge_nested-None-pass]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo.bar.baz)--zab1] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar.baz)--zab1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2] + location: ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\x-\\x-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_compare_types[0-source0-sink0-True] + location: ('tests/test_examples.py', 648, 'test_compare_types[0-source0-sink0-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo['b\\'ar'].baz) $(foo['b\\'ar'].baz)-true true] + location: ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_typechecking[src_type11-sink_type11-merge_flattened-None-pass] + location: ('tests/test_examples.py', 803, 'test_typechecking[src_type11-sink_type11-merge_flattened-None-pass]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo['b\\'ar'].baz) $(foo['b\\'ar'].baz)-true true] + location: ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_compare_types[1-source1-sink1-True] + location: ('tests/test_examples.py', 648, 'test_compare_types[1-source1-sink1-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo.bar.baz)--zab1] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar.baz)--zab1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\x-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo["b\\'ar"].baz) $(foo["b\\'ar"].baz)-true true] + location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type0-sink_type0-None-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type0-sink_type0-None-None-pass]'), 'keywords': {'test_typechecking[src_type0-sink_type0-None-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type0-sink_type0-None-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000973234999946726, 'start': 1685951407.60507, 'stop': 1685951407.606045, '$report_type': 'TestReport', 'item_index': 223, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type0-sink_type0-None-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type0-sink_type0-None-None-pass]'), 'keywords': {'test_typechecking[src_type0-sink_type0-None-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type0-sink_type0-None-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004977159996997216, 'start': 1685951407.606591, 'stop': 1685951407.60709, '$report_type': 'TestReport', 'item_index': 223, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\x-2] + location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: [] [hook] + finish pytest_collection_finish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : DeprecationWarning("the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses"), category : 'DeprecationWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/util/path/__init__.py', lineno : 5, line : None} + nodeid: + when: collect + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : PytestCollectionWarning("cannot collect test class 'TestFsAccess' because it has a __init__ constructor (from: tests/test_path_checks.py)"), category : 'PytestCollectionWarning', filename : '/Users/jasperk/gitlab/cwltool/tests/test_path_checks.py', lineno : 110, line : None} + nodeid: + when: collect + location: None + finish pytest_warning_recorded --> [] [hook] + finish pytest_collection --> None [hook] + pytest_runtestloop [hook] + session: testsfailed=0 testscollected=664> + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_cuda.py::test_cuda_eval_resource_max + location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10238f730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10238f730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_cuda.py::test_cuda_eval_resource_max + location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') + keywords: {'test_cuda_eval_resource_max': 1, 'test_cuda.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0007633309996890603 + start: 1685951407.1543272 + stop: 1685951407.155093 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + early skip of rewriting module: rdflib.plugins.stores.memory [assertion] + early skip of rewriting module: lockfile [assertion] + early skip of rewriting module: lockfile.linklockfile [assertion] + early skip of rewriting module: lockfile.mkdirlockfile [assertion] + early skip of rewriting module: importlib_resources._adapters [assertion] + early skip of rewriting module: importlib_resources.readers [assertion] + early skip of rewriting module: importlib_resources._itertools [assertion] + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10238f730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10238f730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_cuda.py::test_cuda_eval_resource_max + location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') + keywords: {'test_cuda_eval_resource_max': 1, 'test_cuda.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:07]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl'")] + duration: 1.8660347249997358 + start: 1685951407.155669 + stop: 1685951409.021659 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10238f730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10238f730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_cuda.py::test_cuda_eval_resource_max + location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') + keywords: {'test_cuda_eval_resource_max': 1, 'test_cuda.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:07]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl'")] + duration: 0.00017870200008474058 + start: 1685951409.022088 + stop: 1685951409.0222669 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_cuda.py::test_cuda_eval_resource_max + location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_cwl_version.py::test_missing_cwl_version + location: ('tests/test_cwl_version.py', 5, 'test_missing_cwl_version') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10238f730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10238f730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_cwl_version.py::test_missing_cwl_version + location: ('tests/test_cwl_version.py', 5, 'test_missing_cwl_version') + keywords: {'test_missing_cwl_version': 1, 'test_cwl_version.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00023546400007035118 + start: 1685951409.0230908 + stop: 1685951409.023328 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10238f730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10238f730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_cwl_version.py::test_missing_cwl_version + location: ('tests/test_cwl_version.py', 5, 'test_missing_cwl_version') + keywords: {'test_missing_cwl_version': 1, 'test_cwl_version.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/missing_cwlVersion.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing_cwlVersion.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\nNo cwlVersion found. Use the following syntax in your CWL document to declare the version: cwlVersion: .\nNote: if this is a CWL draft-3 (pre v1.0) document then it will need to be upgraded first using https://pypi.org/project/cwl-upgrader/ . 'sbg:draft-2' documents can be upgraded using https://pypi.org/project/sevenbridges-cwl-draft2-upgrader/ .\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/missing_cwlVersion.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing_cwlVersion.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nNo cwlVersion found. Use the following syntax in your CWL document to declare the version: cwlVersion: .\nNote: if this is a CWL draft-3 (pre v1.0) document then it will need to be upgraded first using https://pypi.org/project/cwl-upgrader/ . 'sbg:draft-2' documents can be upgraded using https://pypi.org/project/sevenbridges-cwl-draft2-upgrader/ .")] + duration: 0.021530796000661212 + start: 1685951409.0237088 + stop: 1685951409.0452402 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10238f730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10238f730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_cwl_version.py::test_missing_cwl_version + location: ('tests/test_cwl_version.py', 5, 'test_missing_cwl_version') + keywords: {'test_missing_cwl_version': 1, 'test_cwl_version.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_propert pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_anon_types.py::test_anon_types[snippet1] + location: ('tests/test_anon_types.py', 116, 'test_anon_types[snippet1]') + keywords: {'test_anon_types[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_anon_types.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00022551999973075 + start: 1685951408.172648 + stop: 1685951408.172874 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_anon_types.py::test_anon_types[snippet1] + location: ('tests/test_anon_types.py', 116, 'test_anon_types[snippet1]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_check.py::test_output_checking[tests/wf/badout1.cwl] + location: ('tests/test_check.py', 10, 'test_output_checking[tests/wf/badout1.cwl]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> tests/wf/badout1.cwl [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_check.py::test_output_checking[tests/wf/badout1.cwl] + location: ('tests/test_check.py', 10, 'test_output_checking[tests/wf/badout1.cwl]') + keywords: {'test_output_checking[tests/wf/badout1.cwl]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/badout1.cwl': 1, 'test_check.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00032512599955225596 + start: 1685951408.1741178 + stop: 1685951408.174444 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_check.py::test_output_checking[tests/wf/badout1.cwl] + location: ('tests/test_check.py', 10, 'test_output_checking[tests/wf/badout1.cwl]') + keywords: {'test_output_checking[tests/wf/badout1.cwl]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/badout1.cwl': 1, 'test_check.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/badout1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/badout1.cwl\'\n\x1b[1;30mINFO\x1b[0m [job badout1.cwl] /private/tmp/docker_tmpu35m6j1z$ touch \\\n file1\n\x1b[1;30mERROR\x1b[0m \x1b[31m[job badout1.cwl] Job error:\nError validating output record. Does not exist or is not a File: \'file:///private/tmp/docker_tmpu35m6j1z/file2\'\n in {\n "out": {\n "class": "File",\n "basename": "file2",\n "location": "file:///private/tmp/docker_tmpu35m6j1z/file2",\n "nameroot": "file2",\n "nameext": ""\n }\n}\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job badout1.cwl] completed permanentFail\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/badout1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/badout1.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10238f730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10238f730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_cwl_version.py::test_incorrect_cwl_version + location: ('tests/test_cwl_version.py', 10, 'test_incorrect_cwl_version') + keywords: {'test_incorrect_cwl_version': 1, 'test_cwl_version.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/wrong_cwlVersion.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/wrong_cwlVersion.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\nThe CWL reference runner no longer supports pre CWL v1.0 documents. Supported versions are: \nv1.0\nv1.1\nv1.1.0-dev1 (with --enable-dev flag only)\nv1.2\nv1.2.0-dev1 (with --enable-dev flag only)\nv1.2.0-dev2 (with --enable-dev flag only)\nv1.2.0-dev3 (with --enable-dev flag only)\nv1.2.0-dev4 (with --enable-dev flag only)\nv1.2.0-dev5 (with --enable-dev flag only)\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/wrong_cwlVersion.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/wrong_cwlVersion.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nThe CWL reference runner no longer supports pre CWL v1.0 documents. Supported versions are: \nv1.0\nv1.1\nv1.1.0-dev1 (with --enable-dev flag only)\nv1.2\nv1.2.0-dev1 (with --enable-dev flag only)\nv1.2.0-dev2 (with --enable-dev flag only)\nv1.2.0-dev3 (with --enable-dev flag only)\nv1.2.0-dev4 (with --enable-dev flag only)\nv1.2.0-dev5 (with --enable-dev flag only)")] + duration: 0.0001786439997886191 + start: 1685951409.067976 + stop: 1685951409.0681548 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_cwl_version.py::test_incorrect_cwl_version + location: ('tests/test_cwl_version.py', 10, 'test_incorrect_cwl_version') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_basic[crt_params0] + location: ('tests/test_environment.py', 191, 'test_basic[crt_params0]') + keywords: {'test_basic[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nDEBUG cwltool:job.py:215 [job env3.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjmjn_h8g$ env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjmjn_h8g/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env3.cwl] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjmjn_h8g/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$966de77d2103268fd78d908121525434be2d0ad3",\n "size": 1226,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjvgv7c00\nDEBUG cwltool:job.py:454 [job env3.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryrtx9m3aw\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjmjn_h8g/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjmjn_h8g\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0007479509995391709 + start: 1685951408.8067641 + stop: 1685951408.807515 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_environment.py::test_basic[crt_params0] + location: ('tests/test_environment.py', 191, 'test_basic[crt_params0]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_environment.py::test_basic[crt_params1] + location: ('tests/test_environment.py', 191, 'test_basic[crt_params1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x104cdb9d0> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_basic[crt_params1] + location: ('tests/test_environment.py', 191, 'test_basic[crt_params1]') + keywords: {'test_basic[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0013138579997757915 + start: 1685951408.8089118 + stop: 1685951408.8102279 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_basic[crt_params1] + location: ('tests/test_environment.py', 191, 'test_basic[crt_params1]') + keywords: {'test_basic[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job env3.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_2] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u,target=/hPkhbA \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryufjwpzr8,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryw6annf6u/20230605095011-660582.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/debian:stable-slim \\\n env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1\nINFO cwltool:job.py:905 [job env3.cwl_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job env3.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_2] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$025cbcc94e8ce3a391f3e8dff851c211a1819b4c",\n "size": 113,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_2] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryzd_f_z5e\nDEBUG cwltool:job.py:454 [job env3.cwl_2] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryufjwpzr8\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 3.873030120999829 + start: 1685951408.810559 + stop: 1685951412.6834931 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_basic[crt_params1] + location: ('tests/test_environment.py', 191, 'test_basic[crt_params1]') + keywords: {'test_basic[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job env3.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_2] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u,target=/hPkhbA \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryufjwpzr8,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryw6annf6u/20230605095011-660582.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/debian:stable-slim \\\n env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1\nINFO cwltool:job.py:905 [job env3.cwl_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job env3.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_2] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$025cbcc94e8ce3a391f3e8dff851c211a1819b4c",\n "size": 113,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_2] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryzd_f_z5e\nDEBUG cwltool:job.py:454 [job env3.cwl_2] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryufjwpzr8\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0006656190007561236 + start: 1685951412.684598 + stop: 1685951412.6852648 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_environment.py::test_basic[crt_params1] + location: ('tests/test_environment.py', 191, 'test_basic[crt_params1]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_environment.py::test_basic[crt_params2] + location: ('tests/test_environment.py', 191, 'test_basic[crt_params2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_runtest_makereport [hook] + item: + call: > + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_basic[crt_params2] + location: ('tests/test_environment.py', 191, 'test_basic[crt_params2]') + keywords: {'test_basic[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: skipped + longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_environment.py', 192, 'Skipped: Requires the singularity executable on the system path.') + when: setup + user_properties: [] + sections: [] + duration: 0.0002027240007009823 + start: 1685951412.686377 + stop: 1685951412.68658 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_basic[crt_params2] + location: ('tests/test_environment.py', 191, 'test_basic[crt_params2]') + keywords: {'test_basic[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00015694499961682595 + start: 1685951412.68734 + stop: 1685951412.687498 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_environment.py::test_basic[crt_params2] + location: ('tests/test_environment.py', 191, 'test_basic[crt_params2]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params0] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x104a86740> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params0] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params0]') + keywords: {'test_preserve_single[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0012861739996878896 + start: 1685951412.6882079 + stop: 1685951412.689495 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params0] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params0]') + keywords: {'test_preserve_single[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_3] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nDEBUG cwltool:job.py:215 [job env3.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_3] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf$ env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env3.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_3] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$98d334f5480b7a9c4903726f56fd4214268831dc",\n "size": 1255,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_3] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary_habet66\nDEBUG cwltool:job.py:454 [job env3.cwl_3] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary_jixfjk5\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.7478333760000169 + start: 1685951412.6898298 + stop: 1685951413.4376478 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params0] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params0]') + keywords: {'test_preserve_single[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_3] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nDEBUG cwltool:job.py:215 [job env3.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_3] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf$ env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env3.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_3] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$98d334f5480b7a9c4903726f56fd4214268831dc",\n "size": 1255,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_3] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary_habet66\nDEBUG cwltool:job.py:454 [job env3.cwl_3] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary_jixfjk5\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0005249089999779244 + start: 1685951413.438499 + stop: 1685951413.439025 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params0] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params0]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params1] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x104a86c80> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params1] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params1]') + keywords: {'test_preserve_single[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0019601840003815596 + start: 1685951413.4402938 + stop: 1685951413.442256 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: [] [hook] + pytest_exception_interact [hook] + node: + call: > + report: + finish pytest_exception_interact --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10238f730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10238f730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_dependencies.py::test_biocontainers_resolution + location: ('tests/test_dependencies.py', 44, 'test_biocontainers_resolution') + keywords: {'test_biocontainers_resolution': 1, 'skipif': 1, 'pytestmark': 1, 'test_dependencies.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:11]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/seqtk_seq.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/seqtk_seq.cwl'\n"), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/seqtk_seq.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/seqtk_seq.cwl\'\nERROR galaxy.tool_util.deps.containers:containers.py:283 Could not get container description for tool \'None\'\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/containers.py", line 281, in find_best_container_description\n resolved_container_description = self.resolve(enabled_container_types, tool_info, **kwds)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/containers.py", line 303, in resolve\n container_description = container_resolver.resolve(enabled_container_types, tool_info, install=install, resolution_cache=resolution_cache, session=session)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/container_resolvers/mulled.py", line 465, in resolve\n return docker_cached_container_description(targets, self.namespace, hash_func=self.hash_func, shell=self.shell, resolution_cache=resolution_cache)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/container_resolvers/mulled.py", line 283, in docker_cached_container_description\n cached_images = list_docker_cached_mulled_images(namespace, hash_func=hash_func, resolution_cache=resolution_cache)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/container_resolvers/mulled.py", line 172, in list_docker_cached_mulled_images\n sorted_images = version_sorted([_ for _ in filter(name_filter, images_and_versions)])\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/mulled/util.py", line 185, in version_sorted\n elements = sorted(elements, key=lambda tag: tag.build_string, reverse=True)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/mulled/util.py", line 184, in \n elements = (parse_tag(tag) for tag in elements)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/mulled/util.py", line 178, in parse_tag\n build_string=packaging.version.parse(build_string),\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/packaging/version.py", line 52, in parse\n return Version(version)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/packaging/version.py", line 198, in __init__\n raise InvalidVersion(f"Invalid version: \'{version}\'")\npackaging.version.InvalidVersion: Invalid version: \'pyhdfd78af_0\'')] + duration: 0.0005738190002375632 + start: 1685951411.163533 + stop: 1685951411.164108 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_dependencies.py::test_biocontainers_resolution + location: ('tests/test_dependencies.py', 44, 'test_biocontainers_resolution') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_dependencies.py::test_bioconda + location: ('tests/test_dependencies.py', 109, 'test_bioconda') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + early skip of rewriting module: galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages [assertion] + early skip of rewriting module: galaxy.tool_util.deps.resolvers.conda [assertion] + early skip of rewriting module: galaxy.tool_util.deps.resolvers.homebrew [assertion] + early skip of rewriting module: galaxy.tool_util.deps.resolvers.lmod [assertion] + early skip of rewriting module: galaxy.tool_util.deps.resolvers.modules [assertion] + early skip of rewriting module: galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages [assertion] + pytest_keyboard_interrupt [hook] + excinfo: + finish pytest_keyboard_interrupt --> [] [hook] + pytest_sessionfinish [hook] + session: testsfailed=2 testscollected=664> + exitstatus: 2 + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_sessionfinish --> [] [hook] + pytest_unconfigure [hook] + config: <_pytest.config.Config object at 0x10238f730> + finish pytest_unconfigure --> [] [hook] +DEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_4] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nWARNING cwltool:job.py:657 You have specified \'--preserve-environment={USEDVAR}\' while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility.\nDEBUG cwltool:job.py:215 [job env3.cwl_4] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_4] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez,target=/hPkhbA \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryx954o_yg,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canary5yh9uk_o/20230605095014-057454.cid \\\n --env=USEDVAR=VARVAL \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/debian:stable-slim \\\n env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez/1b478f4af38397731bf74573234c522d361a9eb1\nINFO cwltool:job.py:905 [job env3.cwl_4] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job env3.cwl_4] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_4] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$21616d2e4f8c7185153871c30db9a99dad652ccc",\n "size": 128,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_4] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryybs21h76\nDEBUG cwltool:job.py:454 [job env3.cwl_4] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryx954o_yg\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0007345220001298003 + start: 1685951415.079991 + stop: 1685951415.080726 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params1] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params1]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params2] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_runtest_makereport [hook] + item: + call: > + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params2] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params2]') + keywords: {'test_preserve_single[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: skipped + longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_environment.py', 212, 'Skipped: Requires the singularity executable on the system path.') + when: setup + user_properties: [] + sections: [] + duration: 0.00021694799943361431 + start: 1685951415.081902 + stop: 1685951415.082119 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params2] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params2]') + keywords: {'test_preserve_single[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0001536189993203152 + start: 1685951415.0827148 + stop: 1685951415.08287 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_environment.py::test_preserve_single[crt_params2] + location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params2]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params0] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x104d16950> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params0] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params0]') + keywords: {'test_preserve_all[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.001334257000053185 + start: 1685951415.083617 + stop: 1685951415.084952 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params0] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params0]') + keywords: {'test_preserve_all[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_5] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nDEBUG cwltool:job.py:215 [job env3.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44$ env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env3.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_5] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$58d270332a44ecf9d1615c2977eb9940c22dd22d",\n "size": 4123,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canaryp5usi8w2\nDEBUG cwltool:job.py:454 [job env3.cwl_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canarytlg76wbm\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.5813199350004652 + start: 1685951415.0852869 + stop: 1685951415.666594 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params0] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params0]') + keywords: {'test_preserve_all[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_5] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nDEBUG cwltool:job.py:215 [job env3.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44$ env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env3.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_5] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$58d270332a44ecf9d1615c2977eb9940c22dd22d",\n "size": 4123,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canaryp5usi8w2\nDEBUG cwltool:job.py:454 [job env3.cwl_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canarytlg76wbm\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.000570821999644977 + start: 1685951415.6675022 + stop: 1685951415.668074 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params0] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params0]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params1] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x104d69ab0> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params1] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params1]') + keywords: {'test_preserve_all[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0013532590000977507 + start: 1685951415.669211 + stop: 1685951415.6705651 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + pytest_assertrepr_compare [hook] + config: <_pytest.config.Config object at 0x1021af730> + op: == + left: /Users/jasperk/gitlab/cwltool/venv/bin:/Users/jasperk/.rd/bin:/usr/local/opt/ruby/bin:/Users/jasperk/Applications/Aspera CLI/bin:/usr/local/sbin:/Users/jasperk/mambaforge/bin:/Users/jasperk/mambaforge/condabin:/Users/jasperk/.sdkman/candidates/maven/current/bin:/Users/jasperk/.sdkman/candidates/java/current/bin:/Users/jasperk/.sdkman/candidates/gradle/current/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin://Applications/Topaz Photo AI.app/Contents/Resources/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Applications/COMETS:/Users/jasperk/.krew/bin + right: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin + finish pytest_assertrepr_compare --> [["'/Users/jaspe...erk/.krew/bin' == '/usr/local/s...in:/sbin:/bin'", '- /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', '+ /Users/jasperk/gitlab/cwltool/venv/bin:/Users/jasperk/.rd/bin:/usr/local/opt/ruby/bin:/Users/jasperk/Applications/Aspera CLI/bin:/usr/local/sbin:/Users/jasperk/mambaforge/bin:/Users/jasperk/mambaforge/condabin:/Users/jasperk/.sdkman/candidates/maven/current/bin:/Users/jasperk/.sdkman/candidates/java/current/bin:/Users/jasperk/.sdkman/candidates/gradle/current/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin://Applications/Topaz Photo AI.app/Contents/Resources/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Applications/COMETS:/Users/jasperk/.krew/bin']] [hook] + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params1] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params1]') + keywords: {'test_preserve_all[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nWARNING cwltool:job.py:657 You have specified \'--preserve-entire-environment\' while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility.\nDEBUG cwltool:job.py:215 [job env3.cwl_6] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_6] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek,target=/hPkhbA \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canary3h9ranb8,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canaryyk50isj1/20230605095016-345654.cid \\\n \'--env=PATH=/Users/jasperk/gitlab/cwltool/venv/bin:/Users/jasperk/.rd/bin:/usr/local/opt/ruby/bin:/Users/jasperk/Applications/Aspera CLI/bin:/usr/local/sbin:/Users/jasperk/mambaforge/bin:/Users/jasperk/mambaforge/condabin:/Users/jasperk/.sdkman/candidates/maven/current/bin:/Users/jasperk/.sdkman/candidates/java/current/bin:/Users/jasperk/.sdkman/candidates/gradle/current/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin://Applications/Topaz Photo AI.app/Contents/Resources/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Applications/COMETS:/Users/jasperk/.krew/bin\' \\\n --env=SDKMAN_VERSION=5.18.0 \\\n --env=yodaHost=data.yoda.wur.nl \\\n --env=CONDA_DEFAULT_ENV=base \\\n --env=CONDA_PYTHON_EXE=/Users/jasperk/mambaforge/bin/python \\\n --env=irodsZone=unlock \\\n \'--env=PS1=(venv) \' \\\n --env=CONDA_PREFIX=/Users/jasperk/mambaforge \\\n --env=MAVEN_HOME=/Users/jasperk/.sdkman/candidates/maven/current \\\n --env=yodaAuthScheme=password \\\n --env=yodaSSL=CS_NEG_REQUIRE \\\n --env=LD_LIBRARY_PATH=:/Library/gurobi912/mac64/lib/ \\\n --env=SDKMAN_DIR=/Users/jasperk/.sdkman \\\n --env=GUROBI_COMETS_HOME=/Library/gurobi912/mac64 \\\n --env=LOGNAME=jasperk \\\n --env=PWD=/Users/jasperk/gitlab/cwltool \\\n --env=yodaUserName=jasper.koehorst@wur.nl \\\n --env=PYCHARM_HOSTED=1 \\\n \'--env=PYTHONPATH=/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm:/Users/jasperk/gitlab/cwltool:/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm_matplotlib_backend:/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm_display\' \\\n --env=SHELL=/bin/zsh \\\n --env=PATH_TO_FX=/Applications/javafx-sdk-11.0.2/lib \\\n --env=PAGER=less \\\n --env=WURGITTOKEN=glpat-YvsgD4rxELQmW2KAT7jm \\\n --env=SDKMAN_CANDIDATES_API=https://api.sdkman.io/2 \\\n --env=OLDPWD=/ \\\n --env=ZSH=/Users/jasperk/.oh-my-zsh \\\n --env=TMPDIR=/tmp \\\n \'--env=PYCHARM_HELPERS_DIR=/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm\' \\\n --env=irodsHome=/unlock \\\n --env=VIRTUAL_ENV=/Users/jasperk/gitlab/cwltool/venv \\\n --env=XPC_FLAGS=0x0 \\\n --env=irodsAuthScheme=pam \\\n --env=yodaZone=unlock \\\n --env=yodaCwd=/ \\\n --env=__CF_USER_TEXT_ENCODING=0x1F5:0:0 \\\n --env=irodsCwd=/ \\\n \'--env=CONDA_PROMPT_MODIFIER=(base) \' \\\n --env=LESS=-R \\\n --env=LC_CTYPE=UTF-8 \\\n \'--env=MANPATH=/Users/jasperk/Applications/Aspera CLI/share/man:\' \\\n --env=CONDA_EXE=/Users/jasperk/mambaforge/bin/conda \\\n --env=JAVA_HOME=/Users/jasperk/.sdkman/candidates/java/current \\\n --env=yodaHome=/unlock \\\n --env=COMETS_HOME=/Applications/COMETS \\\n --env=COMMAND_MODE=unix2003 \\\n --env=GRADLE_HOME=/Users/jasperk/.sdkman/candidates/gradle/current \\\n --env=irodsSSL=CS_NEG_REQUIRE \\\n --env=_CE_M= \\\n --env=yodaPort=1247 \\\n --env=XPC_SERVICE_NAME=0 \\\n --env=irodsPort=1247 \\\n --env=CONDA_SHLVL=1 \\\n --env=PYCHARM_DISPLAY_PORT=63342 \\\n --env=SDKMAN_CANDIDATES_DIR=/Users/jasperk/.sdkman/candidates \\\n --env=__CFBundleIdentifier=com.jetbrains.pycharm \\\n --env=CPLEX_STUDIO_DIR221=/Applications/CPLEX_Studio221 \\\n --env=irodsPassword=AWMk9bG21DU94XeuKlYBOPbk881lLEswRMb9HKUUvFAc \\\n --env=LSCOLORS=Gxfxcxdxbxegedabagacad \\\n --env=PYTHONIOENCODING=UTF-8 \\\n --env=PYTEST_RUN_CONFIG=True \\\n --env=SDKMAN_PLATFORM=darwinx64 \\\n --env=USER=jasperk \\\n --env=PATH_TO_FX_MODS=/Applications/javafx-jmods-11.0.2 \\\n --env=yodaPassword=I8-vNP6E-xPE-QrVi85NFFCPuK7fnzbA \\\n --env=irodsUserName=jkoehorst \\\n --env=SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.Ye1Vp6eAdx/Listeners \\\n --env=_CE_CONDA= \\\n --env=PYTHONUNBUFFERED=1 \\\n --env=irodsHost=unlock-icat.irods.surfsara.nl \\\n --env=HOME=/hPkhbA \\\n --env=TEAMCITY_VERSION=LOCAL \\\n --env=_JB_PPRINT_PRIMITIVES=1 \\\n --env=PYTEST_XDIST_TESTRUNUID=ca4970838f1b415dbaafd06f56809891 \\\n --env=PYTEST_XDIST_WORKER=gw2 \\\n --env=PYTEST_XDIST_WORKER_COUNT=8 \\\n \'--env=PYTEST_CURRENT_TEST=tests/test_environment.py::test_preserve_all[crt_params1] (call)\' \\\n --env=USEDVAR=VARVAL \\\n --env=UNUSEDVAR=VARVAL \\\n docker.io/debian:stable-slim \\\n env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1\nINFO cwltool:job.py:905 [job env3.cwl_6] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job env3.cwl_6] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_6] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$89b13cb714abd50b411e8db5fae2226f9942b1aa",\n "size": 3874,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_6] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canaryqq_9yop0\nDEBUG cwltool:job.py:454 [job env3.cwl_6] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canary3h9ranb8\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 1.694537264000246 + start: 1685951415.6709042 + stop: 1685951417.3654 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params1] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params1]') + keywords: {'test_preserve_all[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nWARNING cwltool:job.py:657 You have specified \'--preserve-entire-environment\' while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility.\nDEBUG cwltool:job.py:215 [job env3.cwl_6] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_6] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek,target=/hPkhbA \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canary3h9ranb8,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canaryyk50isj1/20230605095016-345654.cid \\\n \'--env=PATH=/Users/jasperk/gitlab/cwltool/venv/bin:/Users/jasperk/.rd/bin:/usr/local/opt/ruby/bin:/Users/jasperk/Applications/Aspera CLI/bin:/usr/local/sbin:/Users/jasperk/mambaforge/bin:/Users/jasperk/mambaforge/condabin:/Users/jasperk/.sdkman/candidates/maven/current/bin:/Users/jasperk/.sdkman/candidates/java/current/bin:/Users/jasperk/.sdkman/candidates/gradle/current/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin://Applications/Topaz Photo AI.app/Contents/Resources/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Applications/COMETS:/Users/jasperk/.krew/bin\' \\\n --env=SDKMAN_VERSION=5.18.0 \\\n --env=yodaHost=data.yoda.wur.nl \\\n --env=CONDA_DEFAULT_ENV=base \\\n --env=CONDA_PYTHON_EXE=/Users/jasperk/mambaforge/bin/python \\\n --env=irodsZone=unlock \\\n \'--env=PS1=(venv) \' \\\n --env=CONDA_PREFIX=/Users/jasperk/mambaforge \\\n --env=MAVEN_HOME=/Users/jasperk/.sdkman/candidates/maven/current \\\n --env=yodaAuthScheme=password \\\n --env=yodaSSL=CS_NEG_REQUIRE \\\n --env=LD_LIBRARY_PATH=:/Library/gurobi912/mac64/lib/ \\\n --env=SDKMAN_DIR=/Users/jasperk/.sdkman \\\n --env=GUROBI_COMETS_HOME=/Library/gurobi912/mac64 \\\n --env=LOGNAME=jasperk \\\n --env=PWD=/Users/jasperk/gitlab/cwltool \\\n --env=yodaUserName=jasper.koehorst@wur.nl \\\n --env=PYCHARM_HOSTED=1 \\\n \'--env=PYTHONPATH=/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm:/Users/jasperk/gitlab/cwltool:/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm_matplotlib_backend:/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm_display\' \\\n --env=SHELL=/bin/zsh \\\n --env=PATH_TO_FX=/Applications/javafx-sdk-11.0.2/lib \\\n --env=PAGER=less \\\n --env=WURGITTOKEN=glpat-YvsgD4rxELQmW2KAT7jm \\\n --env=SDKMAN_CANDIDATES_API=https://api.sdkman.io/2 \\\n --env=OLDPWD=/ \\\n --env=ZSH=/Users/jasperk/.oh-my-zsh \\\n --env=TMPDIR=/tmp \\\n \'--env=PYCHARM_HELPERS_DIR=/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm\' \\\n --env=irodsHome=/unlock \\\n --env=VIRTUAL_ENV=/Users/jasperk/gitlab/cwltool/venv \\\n --env=XPC_FLAGS=0x0 \\\n --env=irodsAuthScheme=pam \\\n --env=yodaZone=unlock \\\n --env=yodaCwd=/ \\\n --env=__CF_USER_TEXT_ENCODING=0x1F5:0:0 \\\n --env=irodsCwd=/ \\\n \'--env=CONDA_PROMPT_MODIFIER=(base) \' \\\n --env=LESS=-R \\\n --env=LC_CTYPE=UTF-8 \\\n \'--env=MANPATH=/Users/jasperk/Applications/Aspera CLI/share/man:\' \\\n --env=CONDA_EXE=/Users/jasperk/mambaforge/bin/conda \\\n --env=JAVA_HOME=/Users/jasperk/.sdkman/candidates/java/current \\\n --env=yodaHome=/unlock \\\n --env=COMETS_HOME=/Applications/COMETS \\\n --env=COMMAND_MODE=unix2003 \\\n --env=GRADLE_HOME=/Users/jasperk/.sdkman/candidates/gradle/current \\\n --env=irodsSSL=CS_NEG_REQUIRE \\\n --env=_CE_M= \\\n --env=yodaPort=1247 \\\n --env=XPC_SERVICE_NAME=0 \\\n --env=irodsPort=1247 \\\n --env=CONDA_SHLVL=1 \\\n --env=PYCHARM_DISPLAY_PORT=63342 \\\n --env=SDKMAN_CANDIDATES_DIR=/Users/jasperk/.sdkman/candidates \\\n --env=__CFBundleIdentifier=com.jetbrains.pycharm \\\n --env=CPLEX_STUDIO_DIR221=/Applications/CPLEX_Studio221 \\\n --env=irodsPassword=AWMk9bG21DU94XeuKlYBOPbk881lLEswRMb9HKUUvFAc \\\n --env=LSCOLORS=Gxfxcxdxbxegedabagacad \\\n --env=PYTHONIOENCODING=UTF-8 \\\n --env=PYTEST_RUN_CONFIG=True \\\n --env=SDKMAN_PLATFORM=darwinx64 \\\n --env=USER=jasperk \\\n --env=PATH_TO_FX_MODS=/Applications/javafx-jmods-11.0.2 \\\n --env=yodaPassword=I8-vNP6E-xPE-QrVi85NFFCPuK7fnzbA \\\n --env=irodsUserName=jkoehorst \\\n --env=SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.Ye1Vp6eAdx/Listeners \\\n --env=_CE_CONDA= \\\n --env=PYTHONUNBUFFERED=1 \\\n --env=irodsHost=unlock-icat.irods.surfsara.nl \\\n --env=HOME=/hPkhbA \\\n --env=TEAMCITY_VERSION=LOCAL \\\n --env=_JB_PPRINT_PRIMITIVES=1 \\\n --env=PYTEST_XDIST_TESTRUNUID=ca4970838f1b415dbaafd06f56809891 \\\n --env=PYTEST_XDIST_WORKER=gw2 \\\n --env=PYTEST_XDIST_WORKER_COUNT=8 \\\n \'--env=PYTEST_CURRENT_TEST=tests/test_environment.py::test_preserve_all[crt_params1] (call)\' \\\n --env=USEDVAR=VARVAL \\\n --env=UNUSEDVAR=VARVAL \\\n docker.io/debian:stable-slim \\\n env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1\nINFO cwltool:job.py:905 [job env3.cwl_6] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job env3.cwl_6] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_6] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$89b13cb714abd50b411e8db5fae2226f9942b1aa",\n "size": 3874,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_6] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canaryqq_9yop0\nDEBUG cwltool:job.py:454 [job env3.cwl_6] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canary3h9ranb8\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0005804459997307276 + start: 1685951417.366341 + stop: 1685951417.366923 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params1] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params1]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params2] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_runtest_makereport [hook] + item: + call: > + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params2] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params2]') + keywords: {'test_preserve_all[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: skipped + longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_environment.py', 236, 'Skipped: Requires the singularity executable on the system path.') + when: setup + user_properties: [] + sections: [] + duration: 0.00022360500042850617 + start: 1685951417.36818 + stop: 1685951417.368405 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params2] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params2]') + keywords: {'test_preserve_all[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00018487499983166344 + start: 1685951417.369047 + stop: 1685951417.369233 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_environment.py::test_preserve_all[crt_params2] + location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params2]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo)-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> (foo) [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo)-True]') + keywords: {'test_expression_match[(foo)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0005319370002325741 + start: 1685951417.370126 + stop: 1685951417.370659 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo)-True]') + keywords: {'test_expression_match[(foo)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.0002729380003074766 + start: 1685951417.3710022 + stop: 1685951417.3712761 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo)-True]') + keywords: {'test_expression_match[(foo)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00025778500003070803 + start: 1685951417.371628 + stop: 1685951417.3718872 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo)-True]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar)-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> (foo.bar) [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar)-True]') + keywords: {'test_expression_match[(foo.bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0006095749995438382 + start: 1685951417.372681 + stop: 1685951417.373292 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar)-True]') + keywords: {'test_expression_match[(foo.bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.0006968730003791279 + start: 1685951417.374563 + stop: 1685951417.375263 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar)-True]') + keywords: {'test_expression_match[(foo.bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0004372200000943849 + start: 1685951417.375974 + stop: 1685951417.3764129 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar)-True]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'])-True]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> (foo['bar']) [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'])-True]") + keywords: {"test_expression_match[(foo['bar'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0004336890006015892 + start: 1685951417.377285 + stop: 1685951417.37772 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'])-True]") + keywords: {"test_expression_match[(foo['bar'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.0003180759995302651 + start: 1685951417.37807 + stop: 1685951417.378389 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'])-True]") + keywords: {"test_expression_match[(foo['bar'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00027549599963094806 + start: 1685951417.37879 + stop: 1685951417.379067 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'])-True]") + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo["bar"])-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo["bar"])-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> (foo["bar"]) [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo["bar"])-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo["bar"])-True]') + keywords: {'test_expression_match[(foo["bar"])-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo["bar"])-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0006303570007730741 + start: 1685951417.380036 + stop: 1685951417.380668 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo["bar"])-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo["bar"])-True]') + keywords: {'test_expression_match[(foo["bar"])-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo["bar"])-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.00030739700014237314 + start: 1685951417.381089 + stop: 1685951417.381397 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo["bar"])-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo["bar"])-True]') + keywords: {'test_expression_match[(foo["bar"])-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo["bar"])-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00042177999966952484 + start: 1685951417.381833 + stop: 1685951417.382256 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo["bar"])-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo["bar"])-True]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar.baz)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar.baz)-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> (foo.bar.baz) [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar.baz)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar.baz)-True]') + keywords: {'test_expression_match[(foo.bar.baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar.baz)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0004957529999956023 + start: 1685951417.383188 + stop: 1685951417.383685 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar.baz)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar.baz)-True]') + keywords: {'test_expression_match[(foo.bar.baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar.baz)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.0003029549998245784 + start: 1685951417.3841019 + stop: 1685951417.384407 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar.baz)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar.baz)-True]') + keywords: {'test_expression_match[(foo.bar.baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar.baz)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0002607710002848762 + start: 1685951417.384783 + stop: 1685951417.385045 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo.bar.baz)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar.baz)-True]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar'].baz)-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'].baz)-True]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> (foo['bar'].baz) [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar'].baz)-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'].baz)-True]") + keywords: {"test_expression_match[(foo['bar'].baz)-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'].baz)-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0004973000004611094 + start: 1685951417.385895 + stop: 1685951417.386393 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar'].baz)-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'].baz)-True]") + keywords: {"test_expression_match[(foo['bar'].baz)-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'].baz)-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.000273525000011432 + start: 1685951417.386875 + stop: 1685951417.387149 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar'].baz)-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'].baz)-True]") + keywords: {"test_expression_match[(foo['bar'].baz)-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'].baz)-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0005088389998491039 + start: 1685951417.3877451 + stop: 1685951417.388255 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar'].baz)-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'].baz)-True]") + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar']['baz'])-True]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> (foo['bar']['baz']) [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar']['baz'])-True]") + keywords: {"test_expression_match[(foo['bar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0005765379992226372 + start: 1685951417.389447 + stop: 1685951417.390026 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar']['baz'])-True]") + keywords: {"test_expression_match[(foo['bar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.0003066379995289026 + start: 1685951417.39059 + stop: 1685951417.390898 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar']['baz'])-True]") + keywords: {"test_expression_match[(foo['bar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00044312099998933263 + start: 1685951417.391335 + stop: 1685951417.3917801 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['bar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar']['baz'])-True]") + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['b\\'ar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b\\\\'ar']['baz'])-True]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> (foo['b\'ar']['baz']) [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['b\\'ar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b\\\\'ar']['baz'])-True]") + keywords: {"test_expression_match[(foo['b\\\\'ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b\\\\'ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00046658600058435695 + start: 1685951417.392732 + stop: 1685951417.3932002 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['b\\'ar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b\\\\'ar']['baz'])-True]") + keywords: {"test_expression_match[(foo['b\\\\'ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b\\\\'ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.00023022799996397225 + start: 1685951417.393606 + stop: 1685951417.393837 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['b\\'ar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b\\\\'ar']['baz'])-True]") + keywords: {"test_expression_match[(foo['b\\\\'ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b\\\\'ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00024392199975409312 + start: 1685951417.394188 + stop: 1685951417.394433 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['b\\'ar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b\\\\'ar']['baz'])-True]") + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['b ar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b ar']['baz'])-True]") + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> (foo['b ar']['baz']) [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['b ar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b ar']['baz'])-True]") + keywords: {"test_expression_match[(foo['b ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0006260029995246441 + start: 1685951417.395252 + stop: 1685951417.39588 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['b ar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b ar']['baz'])-True]") + keywords: {"test_expression_match[(foo['b ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.0003648389993031742 + start: 1685951417.396404 + stop: 1685951417.39677 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['b ar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b ar']['baz'])-True]") + keywords: {"test_expression_match[(foo['b ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00047715800064906944 + start: 1685951417.397328 + stop: 1685951417.3978071 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo['b ar']['baz'])-True] + location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b ar']['baz'])-True]") + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo_bar)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo_bar)-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> (foo_bar) [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo_bar)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo_bar)-True]') + keywords: {'test_expression_match[(foo_bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo_bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0005532409995794296 + start: 1685951417.399162 + stop: 1685951417.3997161 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo_bar)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo_bar)-True]') + keywords: {'test_expression_match[(foo_bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo_bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.00037115899976924993 + start: 1685951417.400146 + stop: 1685951417.400518 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_expression_match[(foo_bar)-True] + location: ('tests/test_examples.py', 64, 'test_expression_match[(foo_bar)-True]') + keywords: {'test_expression_match[(foo_bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo_bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[]') + keywords: {'test_bad_basecommand_docker[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0006594790002054651 + start: 1685951416.980117 + stop: 1685951416.980778 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[]') + keywords: {'test_bad_basecommand_docker[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\ndocker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_5] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job missing-tool.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_5] /private/tmp/docker_tmpm4eqn0yg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpm4eqn0yg,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmphks0nyni,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmd8b5ps6/20230605095019-182844.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_5] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_5] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_5] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_5] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_5] Removing input staging directory /private/tmp/docker_tmp432ufbfz\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_5] Removing temporary directory /private/tmp/docker_tmphks0nyni\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm4eqn0yg\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] + duration: 3.219032992999928 + start: 1685951416.981208 + stop: 1685951420.2001631 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[]') + keywords: {'test_bad_basecommand_docker[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\ndocker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_5] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job missing-tool.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_5] /private/tmp/docker_tmpm4eqn0yg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpm4eqn0yg,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmphks0nyni,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmd8b5ps6/20230605095019-182844.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_5] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_5] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_5] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_5] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_5] Removing input staging directory /private/tmp/docker_tmp432ufbfz\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_5] Removing temporary directory /private/tmp/docker_tmphks0nyni\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm4eqn0yg\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] + duration: 0.0006168870004330529 + start: 1685951420.2012281 + stop: 1685951420.2018461 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> --parallel [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel]') + keywords: {'test_bad_basecommand_docker[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.000571511000089231 + start: 1685951420.2032309 + stop: 1685951420.203804 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel]') + keywords: {'test_bad_basecommand_docker[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(missing-tool.cwl_6), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job missing-tool.cwl_6] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_6] /private/tmp/docker_tmpgv0ryq66$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpgv0ryq66,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmpg4nxo9cz,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4n_ght97/20230605095020-930474.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_6] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_6] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_6] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_6] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_6] Removing input staging directory /private/tmp/docker_tmpsmvlejwl\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_6] Removing temporary directory /private/tmp/docker_tmpg4nxo9cz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpgv0ryq66\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] + duration: 1.7467867310006113 + start: 1685951420.204257 + stop: 1685951421.9510021 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel]') + keywords: {'test_bad_basecommand_docker[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(missing-tool.cwl_6), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job missing-tool.cwl_6] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_6] /private/tmp/docker_tmpgv0ryq66$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpgv0ryq66,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmpg4nxo9cz,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4n_ght97/20230605095020-930474.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_6] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_6] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_6] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_6] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_6] Removing input staging directory /private/tmp/docker_tmpsmvlejwl\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_6] Removing temporary directory /private/tmp/docker_tmpg4nxo9cz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpgv0ryq66\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] + duration: 0.0006506219997390872 + start: 1685951421.952221 + stop: 1685951421.952873 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--debug] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--debug]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> --debug [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--debug] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--debug]') + keywords: {'test_bad_basecommand_docker[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00046848400052112993 + start: 1685951421.954196 + stop: 1685951421.954665 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--debug] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--debug]') + keywords: {'test_bad_basecommand_docker[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_7] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:job.py:215 [job missing-tool.cwl_7] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_7] /private/tmp/docker_tmpdka9o_pd$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdka9o_pd,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmphj2qch10,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkmoolah4/20230605095022-719860.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_7] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_7] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_7] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_7] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_7] Removing input staging directory /private/tmp/docker_tmp1zqtff0b\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_7] Removing temporary directory /private/tmp/docker_tmphj2qch10\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdka9o_pd\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] + duration: 1.7834863939997376 + start: 1685951421.955127 + stop: 1685951423.73857 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--debug] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--debug]') + keywords: {'test_bad_basecommand_docker[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_7] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:job.py:215 [job missing-tool.cwl_7] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_7] /private/tmp/docker_tmpdka9o_pd$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdka9o_pd,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmphj2qch10,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkmoolah4/20230605095022-719860.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_7] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_7] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_7] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_7] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_7] Removing input staging directory /private/tmp/docker_tmp1zqtff0b\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_7] Removing temporary directory /private/tmp/docker_tmphj2qch10\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdka9o_pd\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] + duration: 0.0006310639992079814 + start: 1685951423.739579 + stop: 1685951423.740211 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--debug] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--debug]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel --debug] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel --debug]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> --parallel --debug [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel --debug] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel --debug]') + keywords: {'test_bad_basecommand_docker[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0008768999996391358 + start: 1685951423.742069 + stop: 1685951423.742949 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel --debug] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel --debug]') + keywords: {'test_bad_basecommand_docker[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_8] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(missing-tool.cwl_8), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job missing-tool.cwl_8] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_8] /private/tmp/docker_tmp7yjsr7dt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp7yjsr7dt,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmpfc4cbkyb,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpm_y03v2j/20230605095024-462520.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_8] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_8] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_8] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_8] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_8] Removing input staging directory /private/tmp/docker_tmpc4xsyrs6\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_8] Removing temporary directory /private/tmp/docker_tmpfc4cbkyb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7yjsr7dt\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] + duration: 1.7442920029998277 + start: 1685951423.743435 + stop: 1685951425.4876852 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel --debug] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel --debug]') + keywords: {'test_bad_basecommand_docker[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_8] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(missing-tool.cwl_8), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job missing-tool.cwl_8] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_8] /private/tmp/docker_tmp7yjsr7dt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp7yjsr7dt,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmpfc4cbkyb,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpm_y03v2j/20230605095024-462520.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_8] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_8] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_8] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_8] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_8] Removing input staging directory /private/tmp/docker_tmpc4xsyrs6\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_8] Removing temporary directory /private/tmp/docker_tmpfc4cbkyb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7yjsr7dt\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] + duration: 0.0006671000001006178 + start: 1685951425.488738 + stop: 1685951425.4894059 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel --debug] + location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel --debug]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_v1_0_position_expression[] + location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_v1_0_position_expression[] + location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[]') + keywords: {'test_v1_0_position_expression[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0005782769994766568 + start: 1685951425.4908118 + stop: 1685951425.491391 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_v1_0_position_expression[] + location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[]') + keywords: {'test_v1_0_position_expression[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1090, in main\n loadingContext, uri = resolve_and_validate_document(\n File "/Users/jasperk/gitlab/cwltool/cwltool/load_tool.py", line 536, in resolve_and_validate_document\n validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/schema.py", line 407, in validate_doc\n raise ValidationException("", None, anyerrors, "*")\nschema_salad.exceptions.ValidationException: tests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int')] + duration: 0.7425466380000216 + start: 1685951425.491789 + stop: 1685951426.234318 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_v1_0_position_expression[] + location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[]') + keywords: {'test_v1_0_position_expression[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1090, in main\n loadingContext, uri = resolve_and_validate_document(\n File "/Users/jasperk/gitlab/cwltool/cwltool/load_tool.py", line 536, in resolve_and_validate_document\n validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/schema.py", line 407, in validate_doc\n raise ValidationException("", None, anyerrors, "*")\nschema_salad.exceptions.ValidationException: tests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int')] + duration: 0.00025266100055887364 + start: 1685951426.234826 + stop: 1685951426.23508 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_v1_0_position_expression[] + location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel] + location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> --parallel [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel] + location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel]') + keywords: {'test_v1_0_position_expression[--parallel]': 1, 'parametrize': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0003147369998259819 + start: 1685951426.235955 + stop: 1685951426.2362711 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel] + location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel]') + keywords: {'test_v1_0_position_expression[--parallel]': 1, 'parametrize': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1090, in main\n loadingContext, uri = resolve_and_validate_document(\n File "/Users/jasperk/gitlab/cwltool/cwltool/load_tool.py", line 536, in resolve_and_validate_document\n validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/schema.py", line 407, in validate_doc\n raise ValidationException("", None, anyerrors, "*")\nschema_salad.exceptions.ValidationException: tests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int')] + duration: 0.7869047670001237 + start: 1685951426.236619 + stop: 1685951427.023506 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel] + location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel]') + keywords: {'test_v1_0_position_expression[--parallel]': 1, 'parametrize': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[]') + keywords: {'test_cid_file_non_existing_dir[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _6] start\nDEBUG cwltool:workflow_job.py:777 [workflow _6] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _6] starting step task1_6\nDEBUG cwltool:workflow_job.py:727 [step task1_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_6] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_6\nDEBUG cwltool:command_line_tool.py:988 [job task1_5] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_5] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir0/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first')] + duration: 0.0011516250006025075 + start: 1685951426.511955 + stop: 1685951426.51311 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> --parallel [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel]') + keywords: {'test_cid_file_non_existing_dir[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0018225509993499145 + start: 1685951426.515224 + stop: 1685951426.517049 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel]') + keywords: {'test_cid_file_non_existing_dir[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step task1_7\nDEBUG cwltool:workflow_job.py:727 [step task1_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_7] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_7\nDEBUG cwltool:command_line_tool.py:988 [job task1_6] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_6), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _7] starting step task2_7\nDEBUG cwltool:workflow_job.py:727 [step task2_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_7] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_7\nDEBUG cwltool:command_line_tool.py:988 [job task2_5] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_6] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_5), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_5] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:executors.py:430 Workflow cannot make any more progress.\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmps3x313_o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpz8kgqzw8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmxatqzqe\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] + duration: 4.700235120999423 + start: 1685951426.517567 + stop: 1685951431.217685 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel]') + keywords: {'test_cid_file_non_existing_dir[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step task1_7\nDEBUG cwltool:workflow_job.py:727 [step task1_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_7] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_7\nDEBUG cwltool:command_line_tool.py:988 [job task1_6] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_6), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _7] starting step task2_7\nDEBUG cwltool:workflow_job.py:727 [step task2_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_7] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_7\nDEBUG cwltool:command_line_tool.py:988 [job task2_5] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_6] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_5), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_5] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:executors.py:430 Workflow cannot make any more progress.\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmps3x313_o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpz8kgqzw8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmxatqzqe\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] + duration: 0.0006869819999337778 + start: 1685951431.218774 + stop: 1685951431.219462 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--debug] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--debug]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir2 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir2 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> --debug [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--debug] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--debug]') + keywords: {'test_cid_file_non_existing_dir[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0018994199999724515 + start: 1685951431.2207181 + stop: 1685951431.2226188 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: [hook] + nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel --debug] + location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel --debug]') + keywords: {'test_v1_0_position_expression[--parallel --debug]': 1, 'parametrize': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1090, in main\n loadingContext, uri = resolve_and_validate_document(\n File "/Users/jasperk/gitlab/cwltool/cwltool/load_tool.py", line 536, in resolve_and_validate_document\n validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/schema.py", line 407, in validate_doc\n raise ValidationException("", None, anyerrors, "*")\nschema_salad.exceptions.ValidationException: tests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int')] + duration: 0.0002695859993764316 + start: 1685951428.471321 + stop: 1685951428.471591 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel --debug] + location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel --debug]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--debug] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--debug]') + keywords: {'test_cid_file_non_existing_dir[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _8] start\nDEBUG cwltool:workflow_job.py:777 [workflow _8] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step task2_8\nDEBUG cwltool:workflow_job.py:727 [step task2_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_8] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_8] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_8\nDEBUG cwltool:command_line_tool.py:988 [job task2_6] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_6] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir2/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first')] + duration: 0.00091174199951638 + start: 1685951432.713697 + stop: 1685951432.7146099 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--debug] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--debug]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> --parallel --debug [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]') + keywords: {'test_cid_file_non_existing_dir[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0015594679998685024 + start: 1685951432.7161012 + stop: 1685951432.7176619 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]') + keywords: {'test_cid_file_non_existing_dir[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task2_9\nDEBUG cwltool:workflow_job.py:727 [step task2_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_9\nDEBUG cwltool:command_line_tool.py:988 [job task2_7] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_7), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task1_9\nDEBUG cwltool:workflow_job.py:727 [step task1_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_9\nDEBUG cwltool:command_line_tool.py:988 [job task1_7] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_7), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_7] initial work dir {}\nDEBUG cwltool:job.py:215 [job task1_7] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:executors.py:430 Workflow cannot make any more progress.\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcznvku2h\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwnjg_83y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa2g7ccv0\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] + duration: 4.7696697329993185 + start: 1685951432.718051 + stop: 1685951437.487604 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]') + keywords: {'test_cid_file_non_existing_dir[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task2_9\nDEBUG cwltool:workflow_job.py:727 [step task2_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\n pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_ext.py::test_warn_large_inputs + location: ('tests/test_ext.py', 264, 'test_warn_large_inputs') + keywords: {'test_warn_large_inputs': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00031238300016411813 + start: 1685951436.9900942 + stop: 1685951436.990408 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_ext.py::test_warn_large_inputs + location: ('tests/test_ext.py', 264, 'test_warn_large_inputs') + keywords: {'test_warn_large_inputs': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{}'), ('Captured stderr call', '/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\'\nWARNING cwltool:process.py:795 tests/wf/listing_v1_0.cwl:5:3: Recursive directory listing has resulted in a large number of File\n objects (5) passed to the input parameter \'d\'. This may negatively\n affect workflow performance and memory use.\n \n If this is a problem, use the hint \'cwltool:LoadListingRequirement\'\n with "shallow_listing" or "no_listing" to change the directory\n listing behavior:\n \n $namespaces:\n cwltool: "http://commonwl.org/cwltool#"\n hints:\n cwltool:LoadListingRequirement:\n loadListing: shallow_listing\n \nDEBUG cwltool:command_line_tool.py:982 [job listing_v1_0.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\nDEBUG cwltool:command_line_tool.py:988 [job listing_v1_0.cwl] {\n "d": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4",\n "basename": "tmp4",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha",\n "basename": "alpha",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta",\n "basename": "delta",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot",\n "basename": "foxtrot",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo",\n "basename": "echo",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker",\n "basename": "baker",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie",\n "basename": "charlie",\n "size": 0\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job listing_v1_0.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4": [\n "/Users/jasperk/gitlab finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') + keywords: {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0016974030004348606 + start: 1685951437.491211 + stop: 1685951437.4929101 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') + keywords: {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task1_10\nDEBUG cwltool:workflow_job.py:727 [step task1_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_10\nDEBUG cwltool:command_line_tool.py:988 [job task1_8] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_8] initial work dir {}\nINFO cwltool:job.py:266 [job task1_8] /private/tmp/docker_tmpqd0zbt01$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqd0zbt01,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwbwvw4vq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095039-089090.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_8] completed success\nDEBUG cwltool:job.py:422 [job task1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqd0zbt01/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_10] completed success\nDEBUG cwltool:job.py:446 [job task1_8] Removing input staging directory /private/tmp/docker_tmpsuq2jbza\nDEBUG cwltool:job.py:454 [job task1_8] Removing temporary directory /private/tmp/docker_tmpwbwvw4vq\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task2_10\nDEBUG cwltool:workflow_job.py:727 [step task2_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_10\nDEBUG cwltool:command_line_tool.py:988 [job task2_8] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_8] initial work dir {}\nINFO cwltool:job.py:266 [job task2_8] /private/tmp/docker_tmpukxzzulb$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpukxzzulb,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp460y3fko,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095040-128027.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_8] completed success\nDEBUG cwltool:job.py:422 [job task2_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpukxzzulb/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_10] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {}\nDEBUG cwltool:job.py:446 [job task2_8] Removing input staging directory /private/tmp/docker_tmp0ewn2kda\nDEBUG cwltool:job.py:454 [job task2_8] Removing temporary directory /private/tmp/docker_tmp460y3fko\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpukxzzulb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqd0zbt01\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6qs7k1_4\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 3.6632841119999284 + start: 1685951437.4933639 + stop: 1685951441.156561 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') + keywords: {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task1_10\nDEBUG cwltool:workflow_job.py:727 [step task1_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_10\nDEBUG cwltool:command_line_tool.py:988 [job task1_8] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_8] initial work dir {}\nINFO cwltool:job.py:266 [job task1_8] /private/tmp/docker_tmpqd0zbt01$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqd0zbt01,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwbwvw4vq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095039-089090.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_8] completed success\nDEBUG cwltool:job.py:422 [job task1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqd0zbt01/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_10] completed success\nDEBUG cwltool:job.py:446 [job task1_8] Removing input staging directory /private/tmp/docker_tmpsuq2jbza\nDEBUG cwltool:job.py:454 [job task1_8] Removing temporary directory /private/tmp/docker_tmpwbwvw4vq\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task2_10\nDEBUG cwltool:workflow_job.py:727 [step task2_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_10\nDEBUG cwltool:command_line_tool.py:988 [job task2_8] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_8] initial work dir {}\nINFO cwltool:job.py:266 [job task2_8] /private/tmp/docker_tmpukxzzulb$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpukxzzulb,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp460y3fko,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095040-128027.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_8] completed success\nDEBUG cwltool:job.py:422 [job task2_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpukxzzulb/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_10] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {}\nDEBUG cwltool:job.py:446 [job task2_8] Removing input staging directory /private/tmp/docker_tmp0ewn2kda\nDEBUG cwltool:job.py:454 [job task2_8] Removing temporary directory /private/tmp/docker_tmp460y3fko\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpukxzzulb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqd0zbt01\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6qs7k1_4\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0008422430000791792 + start: 1685951441.1581 + stop: 1685951441.158945 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> --parallel [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') + keywords: {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0020675499999924796 + start: 1685951441.160426 + stop: 1685951441.162495 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') + keywords: {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_11\nDEBUG cwltool:workflow_job.py:727 [step task2_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_11\nDEBUG cwltool:command_line_tool.py:988 [job task2_9] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_9), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_11\nDEBUG cwltool:workflow_job.py:727 [step task1_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_11\nDEBUG cwltool:command_line_tool.py:988 [job task1_9] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_9] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_9), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task1_9] initial work dir {}\nINFO cwltool:job.py:266 [job task2_9] /private/tmp/docker_tmp6w_kuuwk$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp6w_kuuwk,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpimrbltf0,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-808365.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:266 [job task1_9] /private/tmp/docker_tmpqm8yecor$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqm8yecor,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpxft5vpeu,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-828561.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task2_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_9] completed success\nDEBUG cwltool:job.py:422 [job task2_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6w_kuuwk/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_11] completed success\nDEBUG cwltool:job.py:446 [job task2_9] Removing input staging directory /private/tmp/docker_tmpr2euvrmb\nDEBUG cwltool:job.py:454 [job task2_9] Removing temporary directory /private/tmp/docker_tmpimrbltf0\nINFO cwltool:job.py:905 [job task1_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_9] completed success\nDEBUG cwltool:job.py:422 [job task1_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqm8yecor/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_11] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_9] Removing input staging directory /private/tmp/docker_tmpfumwmmb0\nDEBUG cwltool:job.py:454 [job task1_9] Removing temporary directory /private/tmp/docker_tmpxft5vpeu\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqm8yecor\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp91c3ruq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6w_kuuwk\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 2.689709309999671 + start: 1685951441.163031 + stop: 1685951443.852674 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') + keywords: {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_11\nDEBUG cwltool:workflow_job.py:727 [step task2_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_11\nDEBUG cwltool:command_line_tool.py:988 [job task2_9] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_9), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_11\nDEBUG cwltool:workflow_job.py:727 [step task1_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_11\nDEBUG cwltool:command_line_tool.py:988 [job task1_9] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_9] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_9), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task1_9] initial work dir {}\nINFO cwltool:job.py:266 [job task2_9] /private/tmp/docker_tmp6w_kuuwk$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp6w_kuuwk,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpimrbltf0,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-808365.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:266 [job task1_9] /private/tmp/docker_tmpqm8yecor$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqm8yecor,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpxft5vpeu,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-828561.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task2_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_9] completed success\nDEBUG cwltool:job.py:422 [job task2_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6w_kuuwk/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_11] completed success\nDEBUG cwltool:job.py:446 [job task2_9] Removing input staging directory /private/tmp/docker_tmpr2euvrmb\nDEBUG cwltool:job.py:454 [job task2_9] Removing temporary directory /private/tmp/docker_tmpimrbltf0\nINFO cwltool:job.py:905 [job task1_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_9] completed success\nDEBUG cwltool:job.py:422 [job task1_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqm8yecor/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_11] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_9] Removing input staging directory /private/tmp/docker_tmpfumwmmb0\nDEBUG cwltool:job.py:454 [job task1_9] Removing temporary directory /private/tmp/docker_tmpxft5vpeu\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqm8yecor\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp91c3ruq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6w_kuuwk\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0007029949993011542 + start: 1685951443.85393 + stop: 1685951443.854634 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> --debug [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') + keywords: {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0021138760002941126 + start: 1685951443.8562508 + stop: 1685951443.858367 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') + keywords: {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task2_12\nDEBUG cwltool:workflow_job.py:727 [step task2_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_12\nDEBUG cwltool:command_line_tool.py:988 [job task2_10] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_10] initial work dir {}\nINFO cwltool:job.py:266 [job task2_10] /private/tmp/docker_tmp2edpsbck$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2edpsbck,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwpqrjecs,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095045-366456.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_10] completed success\nDEBUG cwltool:job.py:422 [job task2_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2edpsbck/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_12] completed success\nDEBUG cwltool:job.py:446 [job task2_10] Removing input staging directory /private/tmp/docker_tmpparyqua4\nDEBUG cwltool:job.py:454 [job task2_10] Removing temporary directory /private/tmp/docker_tmpwpqrjecs\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task1_12\nDEBUG cwltool:workflow_job.py:727 [step task1_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_12\nDEBUG cwltool:command_line_tool.py:988 [job task1_10] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_10] initial work dir {}\nINFO cwltool:job.py:266 [job task1_10] /private/tmp/docker_tmpl6uhq9ur$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpl6uhq9ur,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp3v2v_ylx,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095046-398112.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_10] completed success\nDEBUG cwltool:job.py:422 [job task1_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpl6uhq9ur/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_12] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {}\nDEBUG cwltool:job.py:446 [job task1_10] Removing input staging directory /private/tmp/docker_tmp7cq588zt\nDEBUG cwltool:job.py:454 [job task1_10] Removing temporary directory /private/tmp/docker_tmp3v2v_ylx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmbshxay5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpl6uhq9ur\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2edpsbck\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 3.559965896999529 + start: 1685951443.858878 + stop: 1685951447.418756 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') + keywords: {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task2_12\nDEBUG cwltool:workflow_job.py:727 [step task2_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_12\nDEBUG cwltool:command_line_tool.py:988 [job task2_10] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_10] initial work dir {}\nINFO cwltool:job.py:266 [job task2_10] /private/tmp/docker_tmp2edpsbck$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2edpsbck,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwpqrjecs,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095045-366456.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_10] completed success\nDEBUG cwltool:job.py:422 [job task2_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2edpsbck/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_12] completed success\nDEBUG cwltool:job.py:446 [job task2_10] Removing input staging directory /private/tmp/docker_tmpparyqua4\nDEBUG cwltool:job.py:454 [job task2_10] Removing temporary directory /private/tmp/docker_tmpwpqrjecs\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task1_12\nDEBUG cwltool:workflow_job.py:727 [step task1_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_12\nDEBUG cwltool:command_line_tool.py:988 [job task1_10] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_10] initial work dir {}\nINFO cwltool:job.py:266 [job task1_10] /private/tmp/docker_tmpl6uhq9ur$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpl6uhq9ur,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp3v2v_ylx,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095046-398112.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_10] completed success\nDEBUG cwltool:job.py:422 [job task1_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpl6uhq9ur/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_12] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {}\nDEBUG cwltool:job.py:446 [job task1_10] Removing input staging directory /private/tmp/docker_tmp7cq588zt\nDEBUG cwltool:job.py:454 [job task1_10] Removing temporary directory /private/tmp/docker_tmp3v2v_ylx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmbshxay5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpl6uhq9ur\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2edpsbck\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.000630780999927083 + start: 1685951447.419929 + stop: 1685951447.4205608 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> --parallel --debug [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') + keywords: {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0019516170004862943 + start: 1685951447.422921 + stop: 1685951447.424876 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') + keywords: {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task1_13\nDEBUG cwltool:workflow_job.py:727 [step task1_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_13\nDEBUG cwltool:command_line_tool.py:988 [job task1_11] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_11), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task2_13\nDEBUG cwltool:workflow_job.py:727 [step task2_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_13\nDEBUG cwltool:command_line_tool.py:988 [job task2_11] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_11] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_11), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_11] initial work dir {}\nINFO cwltool:job.py:266 [job task1_11] /private/tmp/docker_tmp4m9l14lt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp4m9l14lt,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpexenol_6,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-096004.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:266 [job task2_11] /private/tmp/docker_tmpq2su4gxh$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpq2su4gxh,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmplu6a4tzl,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-110322.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task1_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_11] completed success\nDEBUG cwltool:job.py:422 [job task1_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp4m9l14lt/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_13] completed success\nDEBUG cwltool:job.py:446 [job task1_11] Removing input staging directory /private/tmp/docker_tmpqp3usw7p\nDEBUG cwltool:job.py:454 [job task1_11] Removing temporary directory /private/tmp/docker_tmpexenol_6\nINFO cwltool:job.py:905 [job task2_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_11] completed success\nDEBUG cwltool:job.py:422 [job task2_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpq2su4gxh/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_13] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {}\nDEBUG cwltool:job.py:446 [job task2_11] Removing input staging directory /private/tmp/docker_tmp7r_dkuxt\nDEBUG cwltool:job.py:454 [job task2_11] Removing temporary directory /private/tmp/docker_tmplu6a4tzl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp4m9l14lt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzpg9e3kx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpq2su4gxh\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 2.7110078599998815 + start: 1685951447.425432 + stop: 1685951450.136374 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') + keywords: {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task1_13\nDEBUG cwltool:workflow_job.py:727 [step task1_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_13\nDEBUG cwltool:command_line_tool.py:988 [job task1_11] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_11), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task2_13\nDEBUG cwltool:workflow_job.py:727 [step task2_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_13\nDEBUG cwltool:command_line_tool.py:988 [job task2_11] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_11] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_11), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_11] initial work dir {}\nINFO cwltool:job.py:266 [job task1_11] /private/tmp/docker_tmp4m9l14lt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp4m9l14lt,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpexenol_6,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-096004.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:266 [job task2_11] /private/tmp/docker_tmpq2su4gxh$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpq2su4gxh,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmplu6a4tzl,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-110322.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task1_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_11] completed success\nDEBUG cwltool:job.py:422 [job task1_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp4m9l14lt/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_13] completed success\nDEBUG cwltool:job.py:446 [job task1_11] Removing input staging directory /private/tmp/docker_tmpqp3usw7p\nDEBUG cwltool:job.py:454 [job task1_11] Removing temporary directory /private/tmp/docker_tmpexenol_6\nINFO cwltool:job.py:905 [job task2_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_11] completed success\nDEBUG cwltool:job.py:422 [job task2_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpq2su4gxh/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_13] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {}\nDEBUG cwltool:job.py:446 [job task2_11] Removing input staging directory /private/tmp/docker_tmp7r_dkuxt\nDEBUG cwltool:job.py:454 [job task2_11] Removing temporary directory /private/tmp/docker_tmplu6a4tzl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp4m9l14lt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzpg9e3kx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpq2su4gxh\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0006579000000783708 + start: 1685951450.137392 + stop: 1685951450.138051 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> 그래프 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') + keywords: {'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0021395619996837922 + start: 1685951450.139597 + stop: 1685951450.141738 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') + keywords: {'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "그래프",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmplyn4vznq\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\nDEBUG cwltool:command_line_tool.py:988 [job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script] initial work dir {}\nINFO cwltool:job.py:266 [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script] completed success\nDEBUG cwltool:job.py:422 [job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\nDEBUG cwltool:job.py:454 [job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplyn4vznq\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.7623934020002707 + start: 1685951450.142199 + stop: 1685951450.9045749 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') + keywords: {'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "그래프",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmplyn4vznq\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\nDEBUG cwltool:command_line_tool.py:988 [job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script] initial work dir {}\nINFO cwltool:job.py:266 [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script] completed success\nDEBUG cwltool:job.py:422 [job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\nDEBUG cwltool:job.py:454 [job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplyn4vznq\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0008543869998902665 + start: 1685951450.9057658 + stop: 1685951450.906623 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> график [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') + keywords: {'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0022306440005195327 + start: 1685951450.908751 + stop: 1685951450.910984 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') + keywords: {'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "график",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp44oq2voa\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp44oq2voa\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.7918996069993227 + start: 1685951450.9114509 + stop: 1685951451.7033339 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') + keywords: {'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "график",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp44oq2voa\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp44oq2voa\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0011550549997991766 + start: 1685951451.705198 + stop: 1685951451.7063549 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> ð’ƒ [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') + keywords: {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0022639859998889733 + start: 1685951451.709167 + stop: 1685951451.711433 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') + keywords: {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/%F0%92%81%83",\n "basename": "ð’ƒ",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmppaqyosg7\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppaqyosg7\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.7048519689997192 + start: 1685951451.7120519 + stop: 1685951452.416888 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') + keywords: {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/%F0%92%81%83",\n "basename": "ð’ƒ",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmppaqyosg7\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppaqyosg7\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0006576920004590647 + start: 1685951452.418154 + stop: 1685951452.418813 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> ☕😠[hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') + keywords: {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0023664050004299497 + start: 1685951452.4210129 + stop: 1685951452.423381 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') + keywords: {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/%E2%98%95%F0%9F%98%8D",\n "basename": "☕ðŸ˜",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmptyp89s5l\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptyp89s5l\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.6462540919992534 + start: 1685951452.424056 + stop: 1685951453.070296 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') + keywords: {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/%E2%98%95%F0%9F%98%8D",\n "basename": "☕ðŸ˜",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmptyp89s5l\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptyp89s5l\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0006110310005169595 + start: 1685951453.071579 + stop: 1685951453.072191 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> امتحان [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') + keywords: {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0015628669998477562 + start: 1685951453.07393 + stop: 1685951453.0754938 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') + keywords: {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "امتحان",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpu7fd0k2e\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu7fd0k2e\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.6586480109999684 + start: 1685951453.075871 + stop: 1685951453.734503 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') + keywords: {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "امتحان",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpu7fd0k2e\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu7fd0k2e\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0005586230008702842 + start: 1685951453.7356002 + stop: 1685951453.736159 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> abc+DEFGZ.z_12345- [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') + keywords: {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0013699379996978678 + start: 1685951453.7374332 + stop: 1685951453.7388039 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') + keywords: {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj2n4e2tf\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj2n4e2tf\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.6722589929995593 + start: 1685951453.739232 + stop: 1685951454.411476 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') + keywords: {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj2n4e2tf\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj2n4e2tf\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0010611549996610847 + start: 1685951454.412545 + stop: 1685951454.4136078 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names + location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_clt_returns_specialchar_n0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_clt_returns_specialchar_n0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names + location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') + keywords: {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.001187488999676134 + start: 1685951454.415158 + stop: 1685951454.416346 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names + location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') + keywords: {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.0065578280000408995 + start: 1685951454.416679 + stop: 1685951454.4232378 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names + location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') + keywords: {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0002504579997548717 + start: 1685951454.423627 + stop: 1685951454.423879 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names + location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: -expected1]> + pytest_runtest_logstart [hook] + nodeid: tests/test_pathmapper.py::test_subclass + location: ('tests/test_pathmapper.py', 8, 'test_subclass') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_pathmapper.py::test_subclass + location: ('tests/test_pathmapper.py', 8, 'test_subclass') + keywords: {'test_subclass': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00020675299947470194 + start: 1685951454.4253829 + stop: 1685951454.425591 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_pathmapper.py::test_subclass + location: ('tests/test_pathmapper.py', 8, 'test_subclass') + keywords: {'test_subclass': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.00025883699981932295 + start: 1685951454.4258912 + stop: 1685951454.4261508 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: -expected1]> + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw0/test_relocate_symlinks0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_relocate.py::test_relocate_symlinks + location: ('tests/test_relocate.py', 57, 'test_relocate_symlinks') + keywords: {'test_relocate_symlinks': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0011758240007111453 + start: 1685951453.878428 + stop: 1685951453.8796039 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_relocate.py::test_relocate_symlinks + location: ('tests/test_relocate.py', 57, 'test_relocate_symlinks') + keywords: {'test_relocate_symlinks': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{\n "bar": {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo",\n "basename": "foo",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\ntotal 0\nlrwxr-xr-x 1 jasperk wheel 46 Jun 5 09:50 dir2 -> /Users/jasperk/gitlab/cwltool/tests/reloc/dir2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmphfn_s4u0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\nDEBUG cwltool:command_line_tool.py:988 [job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job test.cwl] completed success\nDEBUG cwltool:job.py:422 [job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\nDEBUG cwltool:job.py:454 [job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmphfn_s4u0\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.7850257770005555 + start: 1685951453.879943 + stop: 1685951454.664951 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_relocate.py::test_relocate_symlinks + location: ('tests/test_relocate.py', 57, 'test_relocate_symlinks') + keywords: {'test_relocate_symlinks': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "bar": {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo",\n "basename": "foo",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\ntotal 0\nlrwxr-xr-x 1 jasperk wheel 46 Jun 5 09:50 dir2 -> /Users/jasperk/gitlab/cwltool/tests/reloc/dir2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmphfn_s4u0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\nDEBUG cwltool:command_line_tool.py:988 [job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job test.cwl] completed success\nDEBUG cwltool:job.py:422 [job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\nDEBUG cwltool:job.py:454 [job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmphfn_s4u0\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0007529229997089715 + start: 1685951454.666344 + stop: 1685951454.667098 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_relocate.py::test_relocate_symlinks + location: ('tests/test_relocate.py', 57, 'test_relocate_symlinks') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_schemadef.py::test_schemadef + location: ('tests/test_schemadef.py', 7, 'test_schemadef') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_schemadef.py::test_schemadef + location: ('tests/test_schemadef.py', 7, 'test_schemadef') + keywords: {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00033530900054756785 + start: 1685951454.669056 + stop: 1685951454.6693928 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_schemadef.py::test_schemadef + location: ('tests/test_schemadef.py', 7, 'test_schemadef') + keywords: {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard")] + duration: 14.348487793000459 + start: 1685951454.6698 + stop: 1685951469.017929 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_schemadef.py::test_schemadef + location: ('tests/test_schemadef.py', 7, 'test_schemadef') + keywords: {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard")] + duration: 0.0002445029995215009 + start: 1685951469.018733 + stop: 1685951469.018979 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_schemadef.py::test_schemadef + location: ('tests/test_schemadef.py', 7, 'test_schemadef') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: -hello bar]> + pytest_runtest_logstart [hook] + nodeid: tests/test_secrets.py::test_obscuring + location: ('tests/test_secrets.py', 24, 'test_obscuring') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> (, {'foo': '(secret-de0c4069-28c0-4d68-919d-2a178da99e07)', 'baz': 'quux'}) [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_secrets.py::test_obscuring + location: ('tests/test_secrets.py', 24, 'test_obscuring') + keywords: {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0003606910004236852 + start: 1685951469.0202398 + stop: 1685951469.020601 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_secrets.py::test_obscuring + location: ('tests/test_secrets.py', 24, 'test_obscuring') + keywords: {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.00022766500023863045 + start: 1685951469.020917 + stop: 1685951469.021145 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: -hello bar]> + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_secrets.py::test_obscuring + location: ('tests/test_secrets.py', 24, 'test_obscuring') + keywords: {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00021421099972940283 + start: 1685951469.021472 + stop: 1685951469.021687 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_secrets.py::test_obscuring + location: ('tests/test_secrets.py', 24, 'test_obscuring') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: -hello bar]> + nextitem: None + pytest_runtest_logstart [hook] + nodeid: tests/test_secrets.py::test_secrets[-hello bar] + location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: -hello bar]> + pytest_fixture_setup [hook] + fixturedef: + request: -hello bar]>> + finish pytest_fixture_setup --> at 0x10fa4a200> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: -hello bar]>> + finish pytest_fixture_setup --> hello bar [hook] + pytest_fixture_setup [hook] + fixturedef: + request: -hello bar]>> + finish pytest_fixture_setup --> (, {'foo': '(secret-89826d56-2552-46d0-8c3c-1d800ae4b08f)', 'baz': 'quux'}) [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: -hello bar]> + call: + finish pytest_runtest_makereport --> -hello bar]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -hello bar]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: -hello bar]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: -hello bar]' when='setup' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_secrets.py::test_secrets[-hello bar] + location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') + keywords: {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0005970800002614851 + start: 1685951469.022847 + stop: 1685951469.023445 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: -hello bar]> + pytest_pyfunc_call [hook] + pyfuncitem: -hello bar]> + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: -hello bar]> + call: + finish pytest_runtest_makereport --> -hello bar]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -hello bar]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: -hello bar]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: -hello bar]' when='call' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_secrets.py::test_secrets[-hello bar] + location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') + keywords: {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.0002542570000514388 + start: 1685951469.023823 + stop: 1685951469.0240781 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: -hello bar]> + nextitem: None + pytest_fixture_post_finalizer [hook] + fixturedef: + request: -hello bar]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: -hello bar]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: -hello bar]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: -hello bar]> + call: + finish pytest_runtest_makereport --> -hello bar]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -hello bar]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: -hello bar]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + report: -hello bar]' when='teardown' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_secrets.py::test_secrets[-hello bar] + location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') + keywords: {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0006589340000573429 + start: 1685951469.0244741 + stop: 1685951469.025135 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_secrets.py::test_secrets[-hello bar] + location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + finish pytest_runtestloop --> True [hook] + pytest_sessionfinish [hook] + session: + exitstatus: 0 + finish pytest_sessionfinish --> [] [hook] + pytest_unconfigure [hook] + config: <_pytest.config.Config object at 0x10d3a7730> + finish pytest_unconfigure --> [] [hook] +e [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_no_output + location: ('tests/test_stdout_stderr_log_dir.py', 22, 'test_log_dir_echo_no_output') + keywords: {'test_log_dir_echo_no_output': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl",\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo] initializing from file:///Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl#echo\nDEBUG cwltool:command_line_tool.py:988 [job echo] {\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n "inp"\n ],\n "datum": "hello"\n }\n]\nDEBUG cwltool:job.py:215 [job echo] initial work dir {}\nINFO cwltool:job.py:266 [job echo] /private/tmp/docker_tmp0vbn7hgf$ echo \\\n hello > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_log_dir_echo_no_output0/echo/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo] completed success\nDEBUG cwltool:job.py:422 [job echo] outputs {}\nDEBUG cwltool:job.py:446 [job echo] Removing input staging directory /private/tmp/docker_tmpcmod_263\nDEBUG cwltool:job.py:454 [job echo] Removing temporary directory /private/tmp/docker_tmpavw9i6k7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0vbn7hgf\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0005319940000845236 + start: 1685951459.2613251 + stop: 1685951459.261858 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_no_output + location: ('tests/test_stdout_stderr_log_dir.py', 22, 'test_log_dir_echo_no_output') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-False-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> False [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-False-True]') + keywords: {'test_input_can_be_named_pipe[True-False-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'True-False-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0015479650000997935 + start: 1685951459.263019 + stop: 1685951459.264568 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-False-True]') + keywords: {'test_input_can_be_named_pipe[True-False-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'True-False-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "streamable": true,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evgsqz7a/stg12438716-31e9-4e5e-870c-e991cb27f8a7/tmp",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\nDEBUG cwltool:command_line_tool.py:988 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "streamable": true,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evgsqz7a/stg12438716-31e9-4e5e-870c-e991cb27f8a7/tmp",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] command line bindings is []')] + duration: 0.0068048149996684515 + start: 1685951459.2649379 + stop: 1685951459.271744 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-False-True]') + keywords: {'test_input_can_be_named_pipe[True-False-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'True-False-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "streamable": true,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evgsqz7a/stg12438716-31e9-4e5e-870c-e991cb27f8a7/tmp",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\nDEBUG cwltool:command_line_tool.py:988 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "streamable": true,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evgsqz7a/stg12438716-31e9-4e5e-870c-e991cb27f8a7/tmp",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] command line bindings is []')] + duration: 0.0006900790003783186 + start: 1685951459.272235 + stop: 1685951459.2729259 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-False-True]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-True-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-True-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> False [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-True-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-True-True]') + keywords: {'test_input_can_be_named_pipe[False-True-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'False-True-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0015698289998908876 + start: 1685951459.274476 + stop: 1685951459.276047 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-True-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-True-True]') + keywords: {'test_input_can_be_named_pipe[False-True-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'False-True-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp",\n "streamable": false,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fjzw5k8w/stg7113322a-d2f3-4f25-a65c-83ff2d4ca310/tmp",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\nDEBUG cwltool:command_line_tool.py:988 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp",\n "streamable": false,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fjzw5k8w/stg7113322a-d2f3-4f25-a65c-83ff2d4ca310/tmp",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] command line bindings is []')] + duration: 0.005819173000418232 + start: 1685951459.2765288 + stop: 1685951459.282349 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-True-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-True-True]') + keywords: {'test_input_can_be_named_pipe[False-True-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'False-True-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp",\n "streamable": false,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fjzw5k8w/stg7113322a-d2f3-4f25-a65c-83ff2d4ca310/tmp",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\nDEBUG cwltool:command_line_tool.py:988 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp",\n "streamable": false,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F0/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fjzw5k8w/stg7113322a-d2f3-4f25-a65c-83ff2d4ca310/tmp",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] command line bindings is []')] + duration: 0.0003800040003625327 + start: 1685951459.2828312 + stop: 1685951459.283212 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-True-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-True-True]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-False-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> False [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> False [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> True [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-False-True]') + keywords: {'test_input_can_be_named_pipe[False-False-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'False-False-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0013823600002069725 + start: 1685951459.2848158 + stop: 1685951459.2862 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-False-True]') + keywords: {'test_input_can_be_named_pipe[False-False-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'False-False-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "streamable": false,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9odb_yg_/stgca46d439-209c-4d1e-bb58-97f4594c7017/tmp",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\nDEBUG cwltool:command_line_tool.py:988 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "streamable": false,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9odb_yg_/stgca46d439-209c-4d1e-bb58-97f4594c7017/tmp",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] command line bindings is []')] + duration: 0.006430190000173752 + start: 1685951459.2866461 + stop: 1685951459.293077 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-False-True]') + keywords: {'test_input_can_be_named_pipe[False-False-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'False-False-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "streamable": false,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9odb_yg_/stgca46d439-209c-4d1e-bb58-97f4594c7017/tmp",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\nDEBUG cwltool:command_line_tool.py:988 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "streamable": false,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9odb_yg_/stgca46d439-209c-4d1e-bb58-97f4594c7017/tmp",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] command line bindings is []')] + duration: 0.0003800060003413819 + start: 1685951459.293602 + stop: 1685951459.293983 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-False-True]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [hook] + baseCommand: echo + class: CommandLineTool + cwlVersion: v1.0 + id: anon_enum_inside_array.cwl + inputs: [{'id': 'anon_enum_inside_array.cwl#first', 'type': {'fields': [{'name': 'anon_enum_inside_array.cwl#first/species', 'type': [{'symbols': ['anon_enum_inside_array.cwl#first/species/homo_sapiens', 'anon_enum_inside_array.cwl#first/species/mus_musculus'], 'type': 'enum'}, 'null']}], 'type': 'record'}}, {'id': 'anon_enum_inside_array.cwl#second', 'type': ['null', {'symbols': ['anon_enum_inside_array.cwl#second/homo_sapiens', 'anon_enum_inside_array.cwl#second/mus_musculus'], 'type': 'enum'}]}] + outputs: [] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') + keywords: {'test_subclass_CLT[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0006368040003508213 + start: 1685951459.294997 + stop: 1685951459.295636 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') + keywords: {'test_subclass_CLT[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.004742043999613088 + start: 1685951459.296237 + stop: 1685951459.300981 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') + keywords: {'test_subclass_CLT[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0002549229993746849 + start: 1685951459.301441 + stop: 1685951459.301697 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [hook] + baseCommand: echo + class: CommandLineTool + cwlVersion: v1.0 + id: anon_enum_inside_array_inside_schemadef.cwl + inputs: [{'id': 'anon_enum_inside_array_inside_schemadef.cwl#first', 'type': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params'}] + outputs: [] + requirements: [{'class': 'SchemaDefRequirement', 'types': [{'fields': [{'name': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build', 'type': ['null', {'symbols': ['anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCh37', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCh38', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCm38'], 'type': 'enum'}]}, {'name': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species', 'type': ['null', {'symbols': ['anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species/homo_sapiens', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species/mus_musculus'], 'type': 'enum'}]}], 'name': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params', 'type': 'record'}]}] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]') + keywords: {'test_subclass_CLT[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00045941999997012317 + start: 1685951459.303957 + stop: 1685951459.3044171 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]') + keywords: {'test_subclass_CLT[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.0067608899998958805 + start: 1685951459.304898 + stop: 1685951459.31166 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]') + keywords: {'test_subclass_CLT[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00024648799990245607 + start: 1685951459.3120792 + stop: 1685951459.312327 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [hook] + baseCommand: echo + class: CommandLineTool + cwlVersion: v1.0 + id: anon_enum_inside_array.cwl + inputs: [{'id': 'anon_enum_inside_array.cwl#first', 'type': {'fields': [{'name': 'anon_enum_inside_array.cwl#first/species', 'type': [{'symbols': ['anon_enum_inside_array.cwl#first/species/homo_sapiens', 'anon_enum_inside_array.cwl#first/species/mus_musculus'], 'type': 'enum'}, 'null']}], 'type': 'record'}}, {'id': 'anon_enum_inside_array.cwl#second', 'type': ['null', {'symbols': ['anon_enum_inside_array.cwl#second/homo_sapiens', 'anon_enum_inside_array.cwl#second/mus_musculus'], 'type': 'enum'}]}] + outputs: [] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') + keywords: {'test_subclass_exprtool[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0003593909996197908 + start: 1685951459.3131678 + stop: 1685951459.313528 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') + keywords: {'test_subclass_exprtool[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.004536303000350017 + start: 1685951459.313875 + stop: 1685951459.318412 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') + keywords: {'test_subclass_exprtool[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0002397010002823663 + start: 1685951459.318814 + stop: 1685951459.3190541 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [hook] + baseCommand: echo + class: CommandLineTool + cwlVersion: v1.0 + id: anon_enum_inside_array_inside_schemadef.cwl + inputs: [{'id': 'anon_enum_inside_array_inside_schemadef.cwl#first', 'type': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params'}] + outputs: [] + requirements: [{'class': 'SchemaDefRequirement', 'types': [{'fields': [{'name': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build', 'type': ['null', {'symbols': ['anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCh37', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCh38', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCm38'], 'type': 'enum'}]}, {'name': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species', 'type': ['null', {'symbols': ['anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species/homo_sapiens', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species/mus_musculus'], 'type': 'enum'}]}], 'name': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params', 'type': 'record'}]}] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') + keywords: {'test_subclass_exprtool[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0003865159997076262 + start: 1685951459.3204029 + stop: 1685951459.32079 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') + keywords: {'test_subclass_exprtool[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.006563943999935873 + start: 1685951459.321141 + stop: 1685951459.327706 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') + keywords: {'test_subclass_exprtool[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00027535600020200945 + start: 1685951459.328183 + stop: 1685951459.328459 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints + location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints + location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') + keywords: {'test_single_process_inherit_reqshints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0013924539998697583 + start: 1685951459.329356 + stop: 1685951459.330749 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints + location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') + keywords: {'test_single_process_inherit_reqshints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp1rf1mf2r$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp1rf1mf2r/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1rf1mf2r/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmpay9r1t0o\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmptl9zl9t0\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1rf1mf2r/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1rf1mf2r\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.823703552000552 + start: 1685951459.3311412 + stop: 1685951460.154825 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints + location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') + keywords: {'test_single_process_inherit_reqshints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp1rf1mf2r$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp1rf1mf2r/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1rf1mf2r/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmpay9r1t0o\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmptl9zl9t0\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1rf1mf2r/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1rf1mf2r\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.000500224999996135 + start: 1685951460.15571 + stop: 1685951460.156211 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints + location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision + location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision + location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') + keywords: {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0018444249999447493 + start: 1685951460.158337 + stop: 1685951460.160183 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision + location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') + keywords: {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl_2] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl_2] /private/tmp/docker_tmp0rf0qbvp$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp0rf0qbvp/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp0rf0qbvp/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl_2] Removing input staging directory /private/tmp/docker_tmpun5mynhb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl_2] Removing temporary directory /private/tmp/docker_tmp2g3z32z6\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0rf0qbvp/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0rf0qbvp\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.9018843539997761 + start: 1685951460.1607418 + stop: 1685951461.062607 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision + location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') + keywords: {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl_2] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl_2] /private/tmp/docker_tmp0rf0qbvp$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp0rf0qbvp/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp0rf0qbvp/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl_2] Removing input staging directory /private/tmp/docker_tmpun5mynhb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl_2] Removing temporary directory /private/tmp/docker_tmp2g3z32z6\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0rf0qbvp/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0rf0qbvp\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0007875250003053225 + start: 1685951461.064188 + stop: 1685951461.064978 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision + location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision + location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision + location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') + keywords: {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0019690780000019004 + start: 1685951461.066408 + stop: 1685951461.068379 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision + location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') + keywords: {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmpug5wf1yr$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpug5wf1yr/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpug5wf1yr/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmpr2_osg12\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpdzs6emmt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpug5wf1yr/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpug5wf1yr\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 1.0924644189999526 + start: 1685951461.068767 + stop: 1685951462.161207 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision + location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') + keywords: {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmpug5wf1yr$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpug5wf1yr/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpug5wf1yr/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmpr2_osg12\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpdzs6emmt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpug5wf1yr/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpug5wf1yr\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.001123591000578017 + start: 1685951462.162127 + stop: 1685951462.163251 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision + location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints + location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints + location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') + keywords: {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.001528846999462985 + start: 1685951462.165597 + stop: 1685951462.1671271 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints + location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') + keywords: {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_no_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_no_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_no_env.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_no_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_no_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_no_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_no_env.cwl] /private/tmp/docker_tmpvp0cy1ef$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpvp0cy1ef/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_no_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_no_env.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpvp0cy1ef/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$ab5f2a9add5f54622dde555ac8ae9a3000e5ee0a",\n "size": 26,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_no_env.cwl] Removing input staging directory /private/tmp/docker_tmp3ef9ddmc\nDEBUG cwltool:job.py:454 [job env-tool2_no_env.cwl] Removing temporary directory /private/tmp/docker_tmp8ts5h8fu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvp0cy1ef/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvp0cy1ef\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.9118393700000524 + start: 1685951462.167519 + stop: 1685951463.079338 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints + location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') + keywords: {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_no_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_no_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_no_env.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_no_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_no_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_no_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_no_env.cwl] /private/tmp/docker_tmpvp0cy1ef$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpvp0cy1ef/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_no_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_no_env.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpvp0cy1ef/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$ab5f2a9add5f54622dde555ac8ae9a3000e5ee0a",\n "size": 26,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_no_env.cwl] Removing input staging directory /private/tmp/docker_tmp3ef9ddmc\nDEBUG cwltool:job.py:454 [job env-tool2_no_env.cwl] Removing temporary directory /private/tmp/docker_tmp8ts5h8fu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvp0cy1ef/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvp0cy1ef\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0006480779993580654 + start: 1685951463.08046 + stop: 1685951463.08111 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints + location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs + location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs + location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') + keywords: {'test_print_targets_embedded_sub_subwfs': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0003258949991504778 + start: 1685951463.0834339 + stop: 1685951463.083762 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs + location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') + keywords: {'test_print_targets_embedded_sub_subwfs': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:924 Input targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 step1 Output targets:\nINFO cwltool:main.py:924 step1 Input targets:\nINFO cwltool:main.py:933 step1 steps targets:\nINFO cwltool:main.py:924 step1/stepX Output targets:\nINFO cwltool:main.py:924 step1/stepX Input targets:\nINFO cwltool:main.py:933 step1/stepX steps targets:\nINFO cwltool:main.py:924 step1/stepX/stepY Output targets:\nINFO cwltool:main.py:924 step1/stepX/stepY Input targets:\nINFO cwltool:main.py:924 step1/stepZ Output targets:\nINFO cwltool:main.py:924 step1/stepZ Input targets:")] + duration: 1.4377574809996077 + start: 1685951463.084152 + stop: 1685951464.521875 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs + location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') + keywords: {'test_print_targets_embedded_sub_subwfs': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:924 Input targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 step1 Output targets:\nINFO cwltool:main.py:924 step1 Input targets:\nINFO cwltool:main.py:933 step1 steps targets:\nINFO cwltool:main.py:924 step1/stepX Output targets:\nINFO cwltool:main.py:924 step1/stepX Input targets:\nINFO cwltool:main.py:933 step1/stepX steps targets:\nINFO cwltool:main.py:924 step1/stepX/stepY Output targets:\nINFO cwltool:main.py:924 step1/stepX/stepY Input targets:\nINFO cwltool:main.py:924 step1/stepZ Output targets:\nINFO cwltool:main.py:924 step1/stepZ Input targets:")] + duration: 0.00038978599968686467 + start: 1685951464.522656 + stop: 1685951464.523047 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs + location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: ]> + pytest_runtest_logstart [hook] + nodeid: tests/test_target.py::test_target_packed + location: ('tests/test_target.py', 29, 'test_target_packed') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_target.py::test_target_packed + location: ('tests/test_target.py', 29, 'test_target_packed') + keywords: {'test_target_packed': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00031677999959356384 + start: 1685951464.524877 + stop: 1685951464.5251951 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_target.py::test_target_packed + location: ('tests/test_target.py', 29, 'test_target_packed') + keywords: {'test_target_packed': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#echo as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmp4ub_5xg8\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpqn2zozpb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxsls6qw3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplfi3vkzu\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 1.532981734000714 + start: 1685951464.525578 + stop: 1685951466.0585248 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: ]> + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_target.py::test_target_packed + location: ('tests/test_target.py', 29, 'test_target_packed') + keywords: {'test_target_packed': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#echo as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmp4ub_5xg8\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpqn2zozpb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxsls6qw3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplfi3vkzu\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0004789479999089963 + start: 1685951466.0598578 + stop: 1685951466.060338 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_target.py::test_target_packed + location: ('tests/test_target.py', 29, 'test_target_packed') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: ]> + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: ]> + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> boolean [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> +#!/usr/bin/env cwl-runner +cwlVersion: v1.0 +class: CommandLineTool +inputs: + - id: bdg + type: "boolean" +outputs: + - id: output + type: File + outputBinding: + glob: foo +baseCommand: + - echo + - "ff" +stdout: foo + [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> at 0x107ca9c60> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: ]' when='setup' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') + keywords: {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.002468566999596078 + start: 1685951466.062423 + stop: 1685951466.064893 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: ]> + pytest_pyfunc_call [hook] + pyfuncitem: ]> + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: ]' when='call' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') + keywords: {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script\n [-h] --bdg [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --bdg\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'")] + duration: 0.6429743959997722 + start: 1685951466.065346 + stop: 1685951466.7083058 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: ]> + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: ]' when='teardown' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') + keywords: {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script\n [-h] --bdg [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --bdg\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'")] + duration: 0.00043712600017897785 + start: 1685951466.709005 + stop: 1685951466.709443 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> [] [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> ['/home/bart/cwl_test/test1'] [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') + keywords: {'test_argparse_append_with_default[job_order0-expected_values0]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order0-expected_values0': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0005423120001069037 + start: 1685951466.713546 + stop: 1685951466.7140899 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') + keywords: {'test_argparse_append_with_default[job_order0-expected_values0]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order0-expected_values0': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")] + duration: 0.9063059879999855 + start: 1685951466.7145128 + stop: 1685951467.6207979 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') + keywords: {'test_argparse_append_with_default[job_order0-expected_values0]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order0-expected_values0': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")] + duration: 0.00041723600043042097 + start: 1685951467.621684 + stop: 1685951467.622103 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: None + pytest_runtest_logstart [hook] + nodeid: tests/test_trs.py::test_workflow_trs_template + location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_trs.py::test_workflow_trs_template + location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') + keywords: {'test_workflow_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0004815839993170812 + start: 1685951467.624228 + stop: 1685951467.624712 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_trs.py::test_workflow_trs_template + location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') + keywords: {'test_workflow_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\nINFO cwltool:load_tool.py:102 Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'")] + duration: 0.6574194070008161 + start: 1685951467.625265 + stop: 1685951468.282669 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: None + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105587730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105587730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_trs.py::test_workflow_trs_template + location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') + keywords: {'test_workflow_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\nINFO cwltool:load_tool.py:102 Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'")] + duration: 0.0025651939995441353 + start: 1685951468.283201 + stop: 1685951468.285768 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_trs.py::test_workflow_trs_template + location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + finish pytest_runtestloop --> True [hook] + pytest_sessionfinish [hook] + session: + exitstatus: 0 + finish pytest_sessionfinish --> [] [hook] + pytest_unconfigure [hook] + config: <_pytest.config.Config object at 0x105587730> + finish pytest_unconfigure --> [] [hook] +eq.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6nz6ufny/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmp4ckaad43\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpzyry0m08\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6nz6ufny/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6nz6ufny\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.843506232999971 + start: 1685951459.815787 + stop: 1685951460.659273 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_collision + location: ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision') + keywords: {'test_single_process_inherit_reqs_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmp6nz6ufny$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp6nz6ufny/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6nz6ufny/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmp4ckaad43\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpzyry0m08\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6nz6ufny/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6nz6ufny\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0006021980007062666 + start: 1685951460.660255 + stop: 1685951460.6608582 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_collision + location: ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision + location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision + location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') + keywords: {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0014790080003876938 + start: 1685951460.662613 + stop: 1685951460.664093 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision + location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') + keywords: {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initializing from _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c\nDEBUG cwltool:command_line_tool.py:988 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "valueFrom": "$(runtime.cores)"\n }\n]\nDEBUG cwltool:job.py:215 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initial work dir {}\nINFO cwltool:job.py:266 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] /private/tmp/docker_tmp0kfy0hx0$ echo \\\n 1 > /private/tmp/docker_tmp0kfy0hx0/cores.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] completed success\nDEBUG cwltool:job.py:422 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp0kfy0hx0/cores.txt",\n "basename": "cores.txt",\n "nameroot": "cores",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing input staging directory /private/tmp/docker_tmpy2q4uxic\nDEBUG cwltool:job.py:454 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing temporary directory /private/tmp/docker_tmp3u7l8gu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0kfy0hx0/cores.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1/cores.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0kfy0hx0\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 1.0293492290002177 + start: 1685951460.664522 + stop: 1685951461.693847 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision + location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') + keywords: {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initializing from _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c\nDEBUG cwltool:command_line_tool.py:988 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "valueFrom": "$(runtime.cores)"\n }\n]\nDEBUG cwltool:job.py:215 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initial work dir {}\nINFO cwltool:job.py:266 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] /private/tmp/docker_tmp0kfy0hx0$ echo \\\n 1 > /private/tmp/docker_tmp0kfy0hx0/cores.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] completed success\nDEBUG cwltool:job.py:422 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp0kfy0hx0/cores.txt",\n "basename": "cores.txt",\n "nameroot": "cores",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing input staging directory /private/tmp/docker_tmpy2q4uxic\nDEBUG cwltool:job.py:454 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing temporary directory /private/tmp/docker_tmp3u7l8gu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0kfy0hx0/cores.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1/cores.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0kfy0hx0\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0005337309994501993 + start: 1685951461.694844 + stop: 1685951461.69538 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision + location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out + location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out + location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') + keywords: {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0026018169992312323 + start: 1685951461.6975958 + stop: 1685951461.7001998 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out + location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') + keywords: {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmp_d17nob5$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp_d17nob5/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfmqmaczt\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7l3r954g\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_d17nob5/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnx7s_q9a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_d17nob5\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 1.0173719809999966 + start: 1685951461.700803 + stop: 1685951462.7181509 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out + location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') + keywords: {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmp_d17nob5$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp_d17nob5/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfmqmaczt\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7l3r954g\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_d17nob5/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnx7s_q9a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_d17nob5\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.00103417099944636 + start: 1685951462.723277 + stop: 1685951462.7243142 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out + location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit + location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit + location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') + keywords: {'test_print_targets_embedded_reqsinherit': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00034795999999914784 + start: 1685951462.72735 + stop: 1685951462.727699 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit + location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') + keywords: {'test_print_targets_embedded_reqsinherit': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/double-nested.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/double-nested.cwl'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 compile Output targets:\nINFO cwltool:main.py:924 compile Input targets:\nINFO cwltool:main.py:933 compile steps targets:\nINFO cwltool:main.py:924 compile/nested_compile Output targets:\nINFO cwltool:main.py:924 compile/nested_compile Input targets:\nINFO cwltool:main.py:933 compile/nested_compile steps targets:\nINFO cwltool:main.py:924 compile/nested_compile/argument Output targets:\nINFO cwltool:main.py:924 compile/nested_compile/argument Input targets:\nINFO cwltool:main.py:924 compile/nested_compile/untar Output targets:\nINFO cwltool:main.py:924 compile/nested_compile/untar Input targets:\nINFO cwltool:main.py:924 create-tar Output targets:")] + duration: 1.7800267129996428 + start: 1685951462.728148 + stop: 1685951464.508131 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit + location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') + keywords: {'test_print_targets_embedded_reqsinherit': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/double-nested.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/double-nested.cwl'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 compile Output targets:\nINFO cwltool:main.py:924 compile Input targets:\nINFO cwltool:main.py:933 compile steps targets:\nINFO cwltool:main.py:924 compile/nested_compile Output targets:\nINFO cwltool:main.py:924 compile/nested_compile Input targets:\nINFO cwltool:main.py:933 compile/nested_compile steps targets:\nINFO cwltool:main.py:924 compile/nested_compile/argument Output targets:\nINFO cwltool:main.py:924 compile/nested_compile/argument Input targets:\nINFO cwltool:main.py:924 compile/nested_compile/untar Output targets:\nINFO cwltool:main.py:924 compile/nested_compile/untar Input targets:\nINFO cwltool:main.py:924 create-tar Output targets:")] + duration: 0.0002299979996678303 + start: 1685951464.5087712 + stop: 1685951464.509002 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit + location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: ]> + pytest_runtest_logstart [hook] + nodeid: tests/test_target.py::test_wrong_target + location: ('tests/test_target.py', 12, 'test_wrong_target') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_target.py::test_wrong_target + location: ('tests/test_target.py', 12, 'test_wrong_target') + keywords: {'test_wrong_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00020157000017206883 + start: 1685951464.510966 + stop: 1685951464.511168 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_target.py::test_wrong_target + location: ('tests/test_target.py', 12, 'test_wrong_target') + keywords: {'test_wrong_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mI'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\nERROR cwltool:main.py:1218 I'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'")] + duration: 1.5277158919998328 + start: 1685951464.511601 + stop: 1685951466.0392802 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: ]> + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_target.py::test_wrong_target + location: ('tests/test_target.py', 12, 'test_wrong_target') + keywords: {'test_wrong_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mI'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\nERROR cwltool:main.py:1218 I'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'")] + duration: 0.00023238100038724951 + start: 1685951466.039777 + stop: 1685951466.040011 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_target.py::test_wrong_target + location: ('tests/test_target.py', 12, 'test_wrong_target') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: ]> + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: ]> + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> help [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> +#!/usr/bin/env cwl-runner +cwlVersion: v1.0 +class: CommandLineTool +doc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)" +inputs: + #Give it a list of input files + - id: input + type: File + inputBinding: + position: 0 +outputs: + - id: output + type: File + outputBinding: + glob: test.txt +stdout: test.txt +baseCommand: [cat] + [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> at 0x1048b93f0> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: ]' when='setup' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') + keywords: {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0021708399999624817 + start: 1685951466.04311 + stop: 1685951466.0452821 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: ]> + pytest_pyfunc_call [hook] + pyfuncitem: ]> + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: ]' when='call' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') + keywords: {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjo7d5ug0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_9] initial work dir {}\nINFO cwltool:job.py:266 [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_9] completed success\nDEBUG cwltool:job.py:422 [job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\nDEBUG cwltool:job.py:454 [job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjo7d5ug0\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.6606748949998291 + start: 1685951466.046178 + stop: 1685951466.70684 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: ]> + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: ]' when='teardown' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') + keywords: {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjo7d5ug0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_9] initial work dir {}\nINFO cwltool:job.py:266 [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_9] completed success\nDEBUG cwltool:job.py:422 [job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\nDEBUG cwltool:job.py:454 [job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjo7d5ug0\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0010807290000229841 + start: 1685951466.7084632 + stop: 1685951466.709545 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparser_without_doc + location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparser_without_doc + location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') + keywords: {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00038347800000337884 + start: 1685951466.7141151 + stop: 1685951466.7145011 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparser_without_doc + location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') + keywords: {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'")] + duration: 0.019146607000038784 + start: 1685951466.715123 + stop: 1685951466.734271 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparser_without_doc + location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') + keywords: {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'")] + duration: 0.00028543000007630326 + start: 1685951466.734833 + stop: 1685951466.7351198 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparser_without_doc + location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_udocker.py::test_udocker_usage_should_not_write_cid_file + location: ('tests/test_udocker.py', 45, 'test_udocker_usage_should_not_write_cid_file') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_runtest_makereport [hook] + item: + call: > + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_udocker.py::test_udocker_usage_should_not_write_cid_file + location: ('tests/test_udocker.py', 45, 'test_udocker_usage_should_not_write_cid_file') + keywords: {'test_udocker_usage_should_not_write_cid_file': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: skipped + longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_udocker.py', 46, 'Skipped: LINUX only') + when: setup + user_properties: [] + sections: [] + duration: 0.0003216280001652194 + start: 1685951466.737472 + stop: 1685951466.737795 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_udocker.py::test_udocker_usage_should_not_write_cid_file + location: ('tests/test_udocker.py', 45, 'test_udocker_usage_should_not_write_cid_file') + keywords: {'test_udocker_usage_should_not_write_cid_file': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00022743400040781125 + start: 1685951466.738656 + stop: 1685951466.7388852 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_udocker.py::test_udocker_usage_should_not_write_cid_file + location: ('tests/test_udocker.py', 45, 'test_udocker_usage_should_not_write_cid_file') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_udocker.py::test_udocker_should_display_memory_usage + location: ('tests/test_udocker.py', 69, 'test_udocker_should_display_memory_usage') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_runtest_makereport [hook] + item: + call: > + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_udocker.py::test_udocker_should_display_memory_usage + location: ('tests/test_udocker.py', 69, 'test_udocker_should_display_memory_usage') + keywords: {'test_udocker_should_display_memory_usage': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: skipped + longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_udocker.py', 70, 'Skipped: Linux only') + when: setup + user_properties: [] + sections: [] + duration: 0.0002621650000946829 + start: 1685951466.741861 + stop: 1685951466.742125 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_udocker.py::test_udocker_should_display_memory_usage + location: ('tests/test_udocker.py', 69, 'test_udocker_should_display_memory_usage') + keywords: {'test_udocker_should_display_memory_usage': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00019226799940952333 + start: 1685951466.7427552 + stop: 1685951466.742949 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_udocker.py::test_udocker_should_display_memory_usage + location: ('tests/test_udocker.py', 69, 'test_udocker_should_display_memory_usage') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_udocker.py::test_udocker_nobanner + location: ('tests/test_udocker.py', 91, 'test_udocker_nobanner') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_runtest_makereport [hook] + item: + call: > + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_udocker.py::test_udocker_nobanner + location: ('tests/test_udocker.py', 91, 'test_udocker_nobanner') + keywords: {'test_udocker_nobanner': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: skipped + longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_udocker.py', 92, 'Skipped: LINUX only') + when: setup + user_properties: [] + sections: [] + duration: 0.00024224099979619496 + start: 1685951466.7450528 + stop: 1685951466.745297 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_udocker.py::test_udocker_nobanner + location: ('tests/test_udocker.py', 91, 'test_udocker_nobanner') + keywords: {'test_udocker_nobanner': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0002610439996715286 + start: 1685951466.7458901 + stop: 1685951466.746152 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_udocker.py::test_udocker_nobanner + location: ('tests/test_udocker.py', 91, 'test_udocker_nobanner') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_validate.py::test_validate_graph_with_no_default + location: ('tests/test_validate.py', 6, 'test_validate_graph_with_no_default') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate.py::test_validate_graph_with_no_default + location: ('tests/test_validate.py', 6, 'test_validate_graph_with_no_default') + keywords: {'test_validate_graph_with_no_default': 1, 'test_validate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0003242369994040928 + start: 1685951466.7482119 + stop: 1685951466.748538 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate.py::test_validate_graph_with_no_default + location: ('tests/test_validate.py', 6, 'test_validate_graph_with_no_default') + keywords: {'test_validate_graph_with_no_default': 1, 'test_validate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl'\nWARNING root:main.py:1124 File contains $graph of multiple objects and no default process (#main). Validating all objects:")] + duration: 0.9934901919996264 + start: 1685951466.7491899 + stop: 1685951467.742657 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate.py::test_validate_graph_with_no_default + location: ('tests/test_validate.py', 6, 'test_validate_graph_with_no_default') + keywords: {'test_validate_graph_with_no_default': 1, 'test_validate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl'\nWARNING root:main.py:1124 File contains $graph of multiple objects and no default process (#main). Validating all objects:")] + duration: 0.00020839900025748648 + start: 1685951467.743108 + stop: 1685951467.743317 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate.py::test_validate_graph_with_no_default + location: ('tests/test_validate.py', 6, 'test_validate_graph_with_no_default') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: None + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_get_expressions + location: ('tests/test_validate_js.py', 24, 'test_get_expressions') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_get_expressions + location: ('tests/test_validate_js.py', 24, 'test_get_expressions') + keywords: {'test_get_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00021349599956010934 + start: 1685951467.7448692 + stop: 1685951467.7450838 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_get_expressions + location: ('tests/test_validate_js.py', 24, 'test_get_expressions') + keywords: {'test_get_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.6003651379996882 + start: 1685951467.7454169 + stop: 1685951468.345769 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: None + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1021af730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_get_expressions + location: ('tests/test_validate_js.py', 24, 'test_get_expressions') + keywords: {'test_get_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0020412240000950987 + start: 1685951468.346211 + stop: 1685951468.348253 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_get_expressions + location: ('tests/test_validate_js.py', 24, 'test_get_expressions') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + finish pytest_runtestloop --> True [hook] + pytest_sessionfinish [hook] + session: + exitstatus: 0 + finish pytest_sessionfinish --> [] [hook] + pytest_unconfigure [hook] + config: <_pytest.config.Config object at 0x1021af730> + finish pytest_unconfigure --> [] [hook] +test_commandLineTool_job_tmpdir_prefix' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_commandLineTool_job_tmpdir_prefix + location: ('tests/test_tmpdir.py', 71, 'test_commandLineTool_job_tmpdir_prefix') + keywords: {'test_commandLineTool_job_tmpdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', '\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] initializing from _:970a4ffb-1255-4205-8526-cc9a0ae3a187\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] initializing from _:970a4ffb-1255-4205-8526-cc9a0ae3a187\nDEBUG cwltool:command_line_tool.py:988 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] command line bindings is []')] + duration: 0.0059925939995082445 + start: 1685951465.111041 + stop: 1685951465.117035 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: ]> + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_commandLineTool_job_tmpdir_prefix + location: ('tests/test_tmpdir.py', 71, 'test_commandLineTool_job_tmpdir_prefix') + keywords: {'test_commandLineTool_job_tmpdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', '\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] initializing from _:970a4ffb-1255-4205-8526-cc9a0ae3a187\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] initializing from _:970a4ffb-1255-4205-8526-cc9a0ae3a187\nDEBUG cwltool:command_line_tool.py:988 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] command line bindings is []')] + duration: 0.00030151900045893854 + start: 1685951465.1175349 + stop: 1685951465.1178381 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_tmpdir.py::test_commandLineTool_job_tmpdir_prefix + location: ('tests/test_tmpdir.py', 71, 'test_commandLineTool_job_tmpdir_prefix') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: ]> + nextitem: ]> + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: ]> + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> foo with c [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: ExpressionTool + +inputs: + foo: + type: + type: record + fields: + one: File + two: string + +expression: $(inputs.foo.two) + +outputs: [] + [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> at 0x107ea1d80> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: ]' when='setup' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00162337599977036 + start: 1685951465.1201751 + stop: 1685951465.1218 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: ]> + pytest_pyfunc_call [hook] + pyfuncitem: ]> + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: ]' when='call' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '"test"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script",\n "foo": {\n "one": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n },\n "two": "test"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpsxld0jq6\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script",\n "foo": {\n "one": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n },\n "two": "test"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsxld0jq6\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.6780413209999097 + start: 1685951465.1225579 + stop: 1685951465.8005838 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: ]> + nextitem: ]> + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: ]' when='teardown' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '"test"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script",\n "foo": {\n "one": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n },\n "two": "test"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpsxld0jq6\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script",\n "foo": {\n "one": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n },\n "two": "test"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsxld0jq6\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0005465860003823764 + start: 1685951465.8011048 + stop: 1685951465.801653 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: ]> + nextitem: ]> + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: ]> + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> foo with d [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: ExpressionTool + +inputs: + foo: + type: + - type: enum + symbols: [cymbal1, cymbal2] + +expression: $(inputs.foo) + +outputs: [] + [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> at 0x107ea1e10> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: ]' when='setup' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.003713201000209665 + start: 1685951465.804359 + stop: 1685951465.808074 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: ]> + pytest_pyfunc_call [hook] + pyfuncitem: ]> + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: ]' when='call' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '"cymbal2"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpqi4cps3i\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqi4cps3i\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.714671594999345 + start: 1685951465.808789 + stop: 1685951466.523444 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: ]> + nextitem: ]> + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: ]' when='teardown' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '"cymbal2"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpqi4cps3i\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqi4cps3i\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.000832688000627968 + start: 1685951466.5242019 + stop: 1685951466.525036 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: ]> + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: ]> + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> foo with e [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: ExpressionTool + +inputs: + foo: File + +expression: '{"bar": $(inputs.foo.location)}' + +outputs: [] + [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> at 0x107ea1ea0> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: ]' when='setup' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0017929050000020652 + start: 1685951466.527004 + stop: 1685951466.5287979 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: ]> + pytest_pyfunc_call [hook] + pyfuncitem: ]> + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: ]' when='call' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '"{\\"bar\\": http://example.com}"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjyzejhiw\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjyzejhiw\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.7014808530002483 + start: 1685951466.5291898 + stop: 1685951467.230655 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: ]> + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: ]' when='teardown' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '"{\\"bar\\": http://example.com}"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjyzejhiw\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjyzejhiw\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0005410029998529353 + start: 1685951467.23134 + stop: 1685951467.231882 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_trs.py::test_tool_trs_template + location: ('tests/test_trs.py', 93, 'test_tool_trs_template') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_trs.py::test_tool_trs_template + location: ('tests/test_trs.py', 93, 'test_tool_trs_template') + keywords: {'test_tool_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00025567400007275864 + start: 1685951467.234224 + stop: 1685951467.2344801 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_trs.py::test_tool_trs_template + location: ('tests/test_trs.py', 93, 'test_tool_trs_template') + keywords: {'test_tool_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\nINFO cwltool:load_tool.py:102 Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'")] + duration: 0.6917008549999082 + start: 1685951467.234879 + stop: 1685951467.9265652 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_trs.py::test_tool_trs_template + location: ('tests/test_trs.py', 93, 'test_tool_trs_template') + keywords: {'test_tool_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\nINFO cwltool:load_tool.py:102 Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'")] + duration: 0.00021415700030047446 + start: 1685951467.9271948 + stop: 1685951467.92741 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_trs.py::test_tool_trs_template + location: ('tests/test_trs.py', 93, 'test_tool_trs_template') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: None + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_js_hint_basic + location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_basic + location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') + keywords: {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0002251839996461058 + start: 1685951467.929321 + stop: 1685951467.929547 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_basic + location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') + keywords: {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.010393084999122948 + start: 1685951467.930013 + stop: 1685951467.940408 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: None + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x105763730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x105763730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_basic + location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') + keywords: {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0015349340001193923 + start: 1685951467.940873 + stop: 1685951467.942409 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_js_hint_basic + location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + finish pytest_runtestloop --> True [hook] + pytest_sessionfinish [hook] + session: + exitstatus: 0 + finish pytest_sessionfinish --> [] [hook] + pytest_unconfigure [hook] + config: <_pytest.config.Config object at 0x105763730> + finish pytest_unconfigure --> [] [hook] +943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}, \'reverse_sort\': True}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b9792322151224743947536605dc9cca24e185d8 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 0b54605194d27895bfbccb163d89b64dba40161d9771e915b204ef89c0501446 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 924e606ff3341e4daea625839633159c1a0c71d12d64532f78160aa03284c5537f3726613c5fa3ec938e0cb3972113e20f4fde6617c88cc98f7e6ec6001e31b5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n },\n "reverse_sort": true\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step rev\nDEBUG cwltool:workflow_job.py:727 [step rev] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step rev] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step rev] start\nDEBUG cwltool:command_line_tool.py:982 [job rev] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/revtool.cwl as part of step rev\nDEBUG cwltool:command_line_tool.py:988 [job rev] {\n "revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job rev] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job rev] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "revtool_input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "dirname": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job rev] initial work dir {}\nINFO cwltool:job.py:266 [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:job.py:905 [job rev] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 97fe1b50b4582cebc7d853796ebd62e3e163aa3f data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nINFO cwltool:job.py:419 [job rev] completed success\nDEBUG cwltool:job.py:422 [job rev] outputs {\n "revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step rev] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:572 [step rev] completed success\nDEBUG cwltool:job.py:446 [job rev] Removing input staging directory /private/tmp/docker_tmp0onaxo3l\nDEBUG cwltool:job.py:454 [job rev] Removing temporary directory /private/tmp/docker_tmpwl097n7z\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step sorted\nDEBUG cwltool:workflow_job.py:727 [step sorted] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step sorted] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:75 [step sorted] start\nDEBUG cwltool:command_line_tool.py:982 [job sorted] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sorttool.cwl as part of step sorted\nDEBUG cwltool:command_line_tool.py:988 [job sorted] {\n "reverse": true,\n "sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job sorted] path mappings is {\n "file:///private/tmp/docker_tmpo8j3qsh0/output.txt": [\n "/private/tmp/docker_tmpo8j3qsh0/output.txt",\n "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job sorted] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sort"\n },\n {\n "position": [\n 1,\n "reverse"\n ],\n "prefix": "--reverse",\n "datum": true\n },\n {\n "position": [\n 2,\n "sorted_input"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1",\n "path": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "dirname": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job sorted] initial work dir {}\nINFO cwltool:job.py:266 [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\nINFO cwltool:job.py:905 [job sorted] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: b9214658cc453331b62c2282b772a5c063dbd284 data/b9/b9214658cc453331b62c2282b772a5c063dbd284\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nINFO cwltool:job.py:419 [job sorted] completed success\nDEBUG cwltool:job.py:422 [job sorted] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step sorted] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step sorted] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:job.py:446 [job sorted] Removing input staging directory /private/tmp/docker_tmpt9i2u3d_\nDEBUG cwltool:job.py:454 [job sorted] Removing temporary directory /private/tmp/docker_tmp7ypgmrbr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplkmwaaf_/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplkmwaaf_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp46e4pq4y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo8j3qsh0\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: df915edbd6b5e75857277eb6c8e1377f0d051ef1 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4e56225fad8da955eebc34f2c094def00b9a7b6b39c500bd4ba036618c22e6f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 42a067ea2914371f209f8c25161dee0d1589e739c64f3275519f23d0af480afc636ea8b3298663632e89b2033c18a855ad9eb5290298ed00837688a946ac1523 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 553157706bf95e14c524a396a623d0f3f87f8ecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c6eccb1bc96bd4f55d03be6f4c0262a736dd8296ecae60d0d403bc9bfc8ca92b metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: f8c2586c8f0749fe5ef9e772f752c63acc2ba9dc8176e2cd8da9e677b952f7ba5a8410f062937ee19a3db25b2a414ef3566294dec7e6b6d011f21d176f3e4e3f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: ca44d2cee82bdf4159a998516a8b7d97de4becde metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 9abbc3a964398906a0a6c446f05be412b4f818c5df80213eefb95585644407f9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4dd04bc545f060056ec3c0eb38c22e70e30c30f4b3d633c60a802e4fcb4607737e7938f57b1eaea5a7044b23bf39461a15ccd68a344564b0a257cb7c966d8562 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b52bb0536caa8678dee76e093bab66c9f6ab72d8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fe046d6822ede74b785f00faa9e38aeeb92d573926c5e8f0dc3e87ddcf655336 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 3fe06b96dca53c5afed7eee93e58b27dd8330c34ce5436271af797259e4ffbc9790bb32f8cdab7244e1a83d0f8f1137464dc0dd757d841ac69412932cf09a9f9 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e58bcf95cb06e3d42132d9c488c389eb62de0170 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 27f34aff0b66f02249b46599489c42e37efc5de28e05274bba403a11a31bd86e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4f70440a6e4c80363471248e4d36d4df1a61f6bdeebdc41391bab98dcc5715361142776d4dd4dcc2b9f81d4687b83ea3a259c4a52374d0e6bed988bb6cfc8683 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: bb4d8f1c88da465df4d205fe71778cf5ee0c971e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 45e8790efb18825deb4c136d97032976f831b167076b31e43bd6ae66fc7466d7 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: bad9c61094a072702da2befe78c06dc406039eba8d4f5abeb39fb0646589428829d6e32ce91b705be4d0b9eba94cad5ca02e0665a23e9190438ef61b05611244 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'sorted_output\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 0536da382206c737b78578fb4cd56d470854cb65 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: ca8f0addfb91188dc24d6f6f2455b58ba794fa05417a99e239993ca8a25627c4 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 1ecd7b38f4685c4c7c7a124deaf30613ef849999f7aa5afb3b537d294a9e66933052c4e35fcb2d7a37e565e33a918c497349b9fc901cf828c5f9cd592dce1114 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: eac590a030efa84e4abe5c70bfbbe059d59cb909 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c85344af5e84a113da5636b4c42935c478fe1b587b2f84f82aa07465a71ce1d1 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fc05d8795084ee56e93edfd135c625c462e71dfaed99a7dc613264eb2b8a75a518580a187fb580fa9309c4cb1398a6501040c6251a221f31cbe67c5576a5d799 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: a7199d53b1f707ab9bfa7a88f832a843a05da1b5 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 44dad89d06c949f171fb43e2c2a870f92520a7d288460cafadfd19afefb7697c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fed9bf631358efdec9cb96154215b41a76dc6b7cd38eeb794f6a94212e5fcf868dcc776b0cec9d950de8370d3e4399a7c36833da2d5bdebfb0e193d813047ad4 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 825bbdb1ae0c5b4dab6115409f478fd2b7546ef1 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 65c5c5444143e944a90a7ec7fed5e89f3b4195f53a84f0747bca4875ad8602ec bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 9212abe820053e53692266203ba3819ceae75bb7f5d82f74281d7d1e9e0682ee506d9b210ef2d2bae5396e8d0f751bafbdf1f361747bf3cdc4d9aaa247919f25 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance')] + duration: 4.937757239000348 + start: 1685951453.6408331 + stop: 1685951458.578468 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_revsort_workflow + location: ('tests/test_provenance.py', 74, 'test_revsort_workflow') + keywords: {'test_revsort_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "sorted_output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt",\n "basename": "output.txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step rev\n\x1b[1;30mINFO\x1b[0m [step rev] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\n\x1b[1;30mINFO\x1b[0m [job rev] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job rev] completed success\n\x1b[1;30mINFO\x1b[0m [step rev] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step sorted\n\x1b[1;30mINFO\x1b[0m [step sorted] start\n\x1b[1;30mINFO\x1b[0m [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\n\x1b[1;30mINFO\x1b[0m [job sorted] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job sorted] completed success\n\x1b[1;30mINFO\x1b[0m [step sorted] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\', job_order=[\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}, \'reverse_sort\': True}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b9792322151224743947536605dc9cca24e185d8 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 0b54605194d27895bfbccb163d89b64dba40161d9771e915b204ef89c0501446 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 924e606ff3341e4daea625839633159c1a0c71d12d64532f78160aa03284c5537f3726613c5fa3ec938e0cb3972113e20f4fde6617c88cc98f7e6ec6001e31b5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n },\n "reverse_sort": true\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step rev\nDEBUG cwltool:workflow_job.py:727 [step rev] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step rev] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step rev] start\nDEBUG cwltool:command_line_tool.py:982 [job rev] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/revtool.cwl as part of step rev\nDEBUG cwltool:command_line_tool.py:988 [job rev] {\n "revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job rev] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job rev] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "revtool_input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "dirname": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job rev] initial work dir {}\nINFO cwltool:job.py:266 [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:job.py:905 [job rev] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 97fe1b50b4582cebc7d853796ebd62e3e163aa3f data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nINFO cwltool:job.py:419 [job rev] completed success\nDEBUG cwltool:job.py:422 [job rev] outputs {\n "revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step rev] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:572 [step rev] completed success\nDEBUG cwltool:job.py:446 [job rev] Removing input staging directory /private/tmp/docker_tmp0onaxo3l\nDEBUG cwltool:job.py:454 [job rev] Removing temporary directory /private/tmp/docker_tmpwl097n7z\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step sorted\nDEBUG cwltool:workflow_job.py:727 [step sorted] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step sorted] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:75 [step sorted] start\nDEBUG cwltool:command_line_tool.py:982 [job sorted] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sorttool.cwl as part of step sorted\nDEBUG cwltool:command_line_tool.py:988 [job sorted] {\n "reverse": true,\n "sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job sorted] path mappings is {\n "file:///private/tmp/docker_tmpo8j3qsh0/output.txt": [\n "/private/tmp/docker_tmpo8j3qsh0/output.txt",\n "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job sorted] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sort"\n },\n {\n "position": [\n 1,\n "reverse"\n ],\n "prefix": "--reverse",\n "datum": true\n },\n {\n "position": [\n 2,\n "sorted_input"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1",\n "path": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "dirname": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job sorted] initial work dir {}\nINFO cwltool:job.py:266 [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\nINFO cwltool:job.py:905 [job sorted] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: b9214658cc453331b62c2282b772a5c063dbd284 data/b9/b9214658cc453331b62c2282b772a5c063dbd284\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nINFO cwltool:job.py:419 [job sorted] completed success\nDEBUG cwltool:job.py:422 [job sorted] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step sorted] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step sorted] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:job.py:446 [job sorted] Removing input staging directory /private/tmp/docker_tmpt9i2u3d_\nDEBUG cwltool:job.py:454 [job sorted] Removing temporary directory /private/tmp/docker_tmp7ypgmrbr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplkmwaaf_/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplkmwaaf_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp46e4pq4y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo8j3qsh0\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: df915edbd6b5e75857277eb6c8e1377f0d051ef1 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4e56225fad8da955eebc34f2c094def00b9a7b6b39c500bd4ba036618c22e6f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 42a067ea2914371f209f8c25161dee0d1589e739c64f3275519f23d0af480afc636ea8b3298663632e89b2033c18a855ad9eb5290298ed00837688a946ac1523 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 553157706bf95e14c524a396a623d0f3f87f8ecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c6eccb1bc96bd4f55d03be6f4c0262a736dd8296ecae60d0d403bc9bfc8ca92b metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: f8c2586c8f0749fe5ef9e772f752c63acc2ba9dc8176e2cd8da9e677b952f7ba5a8410f062937ee19a3db25b2a414ef3566294dec7e6b6d011f21d176f3e4e3f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: ca44d2cee82bdf4159a998516a8b7d97de4becde metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 9abbc3a964398906a0a6c446f05be412b4f818c5df80213eefb95585644407f9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4dd04bc545f060056ec3c0eb38c22e70e30c30f4b3d633c60a802e4fcb4607737e7938f57b1eaea5a7044b23bf39461a15ccd68a344564b0a257cb7c966d8562 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b52bb0536caa8678dee76e093bab66c9f6ab72d8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fe046d6822ede74b785f00faa9e38aeeb92d573926c5e8f0dc3e87ddcf655336 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 3fe06b96dca53c5afed7eee93e58b27dd8330c34ce5436271af797259e4ffbc9790bb32f8cdab7244e1a83d0f8f1137464dc0dd757d841ac69412932cf09a9f9 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e58bcf95cb06e3d42132d9c488c389eb62de0170 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 27f34aff0b66f02249b46599489c42e37efc5de28e05274bba403a11a31bd86e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4f70440a6e4c80363471248e4d36d4df1a61f6bdeebdc41391bab98dcc5715361142776d4dd4dcc2b9f81d4687b83ea3a259c4a52374d0e6bed988bb6cfc8683 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: bb4d8f1c88da465df4d205fe71778cf5ee0c971e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 45e8790efb18825deb4c136d97032976f831b167076b31e43bd6ae66fc7466d7 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: bad9c61094a072702da2befe78c06dc406039eba8d4f5abeb39fb0646589428829d6e32ce91b705be4d0b9eba94cad5ca02e0665a23e9190438ef61b05611244 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'sorted_output\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 0536da382206c737b78578fb4cd56d470854cb65 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: ca8f0addfb91188dc24d6f6f2455b58ba794fa05417a99e239993ca8a25627c4 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 1ecd7b38f4685c4c7c7a124deaf30613ef849999f7aa5afb3b537d294a9e66933052c4e35fcb2d7a37e565e33a918c497349b9fc901cf828c5f9cd592dce1114 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: eac590a030efa84e4abe5c70bfbbe059d59cb909 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c85344af5e84a113da5636b4c42935c478fe1b587b2f84f82aa07465a71ce1d1 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fc05d8795084ee56e93edfd135c625c462e71dfaed99a7dc613264eb2b8a75a518580a187fb580fa9309c4cb1398a6501040c6251a221f31cbe67c5576a5d799 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: a7199d53b1f707ab9bfa7a88f832a843a05da1b5 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 44dad89d06c949f171fb43e2c2a870f92520a7d288460cafadfd19afefb7697c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fed9bf631358efdec9cb96154215b41a76dc6b7cd38eeb794f6a94212e5fcf868dcc776b0cec9d950de8370d3e4399a7c36833da2d5bdebfb0e193d813047ad4 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 825bbdb1ae0c5b4dab6115409f478fd2b7546ef1 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 65c5c5444143e944a90a7ec7fed5e89f3b4195f53a84f0747bca4875ad8602ec bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 9212abe820053e53692266203ba3819ceae75bb7f5d82f74281d7d1e9e0682ee506d9b210ef2d2bae5396e8d0f751bafbdf1f361747bf3cdc4d9aaa247919f25 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance')] + duration: 0.0007942510001157643 + start: 1685951458.580619 + stop: 1685951458.581415 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_revsort_workflow + location: ('tests/test_provenance.py', 74, 'test_revsort_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + nodeid: tests/test_provenance.py::test_revsort_workflow + when: runtest + location: None + finish pytest_warning_recorded --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut + location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut + location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') + keywords: {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0014417179991141893 + start: 1685951458.583897 + stop: 1685951458.5853388 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + pytest_assertrepr_compare [hook] + config: <_pytest.config.Config object at 0x1043f7730> + op: == + left: 1 + right: 0 + finish pytest_assertrepr_compare --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: > + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut + location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') + keywords: {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: failed + longrepr: {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 46, 'message': "AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))\nassert 1 == 0"}, 'reprtraceback': {'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_revsort_workflow_shortcut(tmp_path: Path) -> None:', ' """Confirm that using \'cwl:tool\' shortcut still snapshots the CWL files."""', '> folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/revsort-job-shortcut.json"),', ' )'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 89, 'message': ''}, 'style': 'long'}}, {'type': 'ReprEntry', 'data': {'lines': [' def cwltool(tmp_path: Path, *args: Any) -> Path:', ' prov_folder = tmp_path / "provenance"', ' prov_folder.mkdir()', ' new_args = ["--provenance", str(prov_folder)]', ' new_args.extend(args)', ' # Run within a temporary directory to not pollute git checkout', ' tmp_dir = tmp_path / "cwltool-run"', ' tmp_dir.mkdir()', ' with working_directory(tmp_dir):', ' status = main(new_args)', '> assert status == 0, f"Failed: cwltool.main({args})"', "E AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))", 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')"), ('args', "('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',)"), ('prov_folder', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')"), ('new_args', "['--provenance', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance', '/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json']"), ('tmp_dir', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 46, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, 'sections': [], 'chain': [({'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_revsort_workflow_shortcut(tmp_path: Path) -> None:', ' """Confirm that using \'cwl:tool\' shortcut still snapshots the CWL files."""', '> folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/revsort-job-shortcut.json"),', ' )'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 89, 'message': ''}, 'style': 'long'}}, {'type': 'ReprEntry', 'data': {'lines': [' def cwltool(tmp_path: Path, *args: Any) -> Path:', ' prov_folder = tmp_path / "provenance"', ' prov_folder.mkdir()', ' new_args = ["--provenance", str(prov_folder)]', ' new_args.extend(args)', ' # Run within a temporary directory to not pollute git checkout', ' tmp_dir = tmp_path / "cwltool-run"', ' tmp_dir.mkdir()', ' with working_directory(tmp_dir):', ' status = main(new_args)', '> assert status == 0, f"Failed: cwltool.main({args})"', "E AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))", 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')"), ('args', "('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',)"), ('prov_folder', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')"), ('new_args', "['--provenance', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance', '/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json']"), ('tmp_dir', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 46, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 46, 'message': "AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))\nassert 1 == 0"}, None)]} + when: call + user_properties: [] + sections: [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mERROR\x1b[0m \x1b[31mGot workflow error\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json",\n "reverse_sort": true,\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "@id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'reverse_sort\': True, \'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 5e5a492f53d25bdd4e5e7e3ee61407036d74c263 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 8322e8a8c8231f681484b7cf2caae8110994310a49cbb0679a9dc40993bd863d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 57b1439b4885ea2220eb4b4177e0c82d5724d29dd75ce4ce5b4041c9a9c705cadc478ed732165222d7fff8788ef51dc4c5478ae1586d34fa3bec637b183cdcd6 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nERROR cwltool:executors.py:250 Got workflow error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: d4e780eac6b995170c5544138e51cee42bf82b02 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 71854d40af17ddaad25710ff92bed3033edc5312cea32640d1780241b99df51f metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: ba634748b2a242590fe4f2f293ea32ab4cae028fc7ba9a83b3ce2964374030766b9b71e13fe231a9e27877e79b5c939c949ce2cab6806a002f4ef8005ea34504 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: fa166224b2884b8c1a7019701241269f0fe8f4ba metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: b220ef2e9661453dc089f3645d905eb38ede5f81267288875ebaa393f440a3b6 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 67dc40c370f4eb425ad35887933493d90057b10fb0d6c65a7b9dd47fd482ce515036fe98304f7a6254891a4240f1f515e792dd7c3610f9d4e38c5954de185854 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 7b845a04531a0aea8b66445b3cb5dfd3cc38987e bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 674fc7391ca2a9c892cc4a7b8f6d69ef84f4debea78506708c389a4611090a94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 350e30ea50137627007116ea6a7b9e3f71a7b9e01835e5e0b82201f45bd7f577cc3f294c98401c2afabc72bd7c331d4a7ad8cb70dcac056749b3d897311a5e03 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')] + duration: 0.9283330289999867 + start: 1685951458.585697 + stop: 1685951459.514008 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_exception_interact [hook] + node: + call: > + report: + finish pytest_exception_interact --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut + location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') + keywords: {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mERROR\x1b[0m \x1b[31mGot workflow error\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json",\n "reverse_sort": true,\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "@id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'reverse_sort\': True, \'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 5e5a492f53d25bdd4e5e7e3ee61407036d74c263 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 8322e8a8c8231f681484b7cf2caae8110994310a49cbb0679a9dc40993bd863d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 57b1439b4885ea2220eb4b4177e0c82d5724d29dd75ce4ce5b4041c9a9c705cadc478ed732165222d7fff8788ef51dc4c5478ae1586d34fa3bec637b183cdcd6 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nERROR cwltool:executors.py:250 Got workflow error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: d4e780eac6b995170c5544138e51cee42bf82b02 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 71854d40af17ddaad25710ff92bed3033edc5312cea32640d1780241b99df51f metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: ba634748b2a242590fe4f2f293ea32ab4cae028fc7ba9a83b3ce2964374030766b9b71e13fe231a9e27877e79b5c939c949ce2cab6806a002f4ef8005ea34504 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: fa166224b2884b8c1a7019701241269f0fe8f4ba metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: b220ef2e9661453dc089f3645d905eb38ede5f81267288875ebaa393f440a3b6 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 67dc40c370f4eb425ad35887933493d90057b10fb0d6c65a7b9dd47fd482ce515036fe98304f7a6254891a4240f1f515e792dd7c3610f9d4e38c5954de185854 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 7b845a04531a0aea8b66445b3cb5dfd3cc38987e bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 674fc7391ca2a9c892cc4a7b8f6d69ef84f4debea78506708c389a4611090a94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 350e30ea50137627007116ea6a7b9e3f71a7b9e01835e5e0b82201f45bd7f577cc3f294c98401c2afabc72bd7c331d4a7ad8cb70dcac056749b3d897311a5e03 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')] + duration: 0.0016798560000097496 + start: 1685951459.699641 + stop: 1685951459.701323 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut + location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_nested_workflow + location: ('tests/test_provenance.py', 98, 'test_nested_workflow') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_nested_workflow + location: ('tests/test_provenance.py', 98, 'test_nested_workflow') + keywords: {'test_nested_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0018565800000942545 + start: 1685951459.703209 + stop: 1685951459.705068 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_nested_workflow + location: ('tests/test_provenance.py', 98, 'test_nested_workflow') + keywords: {'test_nested_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{\n "classout": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class",\n "basename": "Hello.class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _18] start\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step create-tar\n\x1b[1;30mINFO\x1b[0m [step create-tar] start\n\x1b[1;30mINFO\x1b[0m [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nMon Jun 5 09:51:00 CEST 2023\nMon Jun 5 09:51:00 CEST 2023\n\x1b[1;30mINFO\x1b[0m [job create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [step create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step compile\n\x1b[1;30mINFO\x1b[0m [step compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step untar\n\x1b[1;30mINFO\x1b[0m [step untar] start\n\x1b[1;30mINFO\x1b[0m [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\n\x1b[1;30mINFO\x1b[0m [job untar] completed success\n\x1b[1;30mINFO\x1b[0m [step untar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step argument\n\x1b[1;30mINFO\x1b[0m [step argument] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/openjdk:9.0.1-11-slim']\n9.0.1-11-slim: Pulling from library/openjdk\nDigest: sha256:dc239c9a17aa509d4e79dc4980e40a5f0c8af78a9bcefab2b5eedf819f702298\nStatus: Image is up to date for openjdk:9.0.1-11-slim\ndocker.io/library/openjdk:9.0.1-11-slim\n\x1b[1;30mINFO\x1b[0m [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\n\x1b[1;30mINFO\x1b[0m [job argument] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job argument] completed success\n\x1b[1;30mINFO\x1b[0m [step argument] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] completed success\n\x1b[1;30mINFO\x1b[0m [step compile] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 74ece951469a5306ac6512cff2a9f3b25b91c858 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: a0f6fb34d0ba97018b294486569ded02bb6e6e659d3e06c5de4f214582691f36 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: f0dca2f20d6e9cd7b5ca6e9ea53e3c5548164e2b77ca0b2a1f3e785ce12f314ca29d1943f80ee974373ab7ead0031aee08c07bb511c34c82cc951e3bef28c9b0 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _18] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile not ready\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step create-tar\nDEBUG cwltool:workflow_job.py:727 [step create-tar] job input {}\nDEBUG cwltool:workflow_job.py:732 [step create-tar] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step create-tar] start\nDEBUG cwltool:command_line_tool.py:982 [job create-tar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/fbd87079-fe0c-4de9-b99f-0c79323cf2c1 as part of step create-tar\nDEBUG cwltool:command_line_tool.py:988 [job create-tar] {}\nDEBUG cwltool:command_line_tool.py:1000 [job create-tar] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job create-tar] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "date\\ntar cf hello.tar Hello.java\\ndate\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job create-tar] initial work dir {\n "_:5de9498b-d23e-4bbf-b5e6-3d9459eedb80": [\n "public class Hello {\\n public static void main(String[] argv) {\\n System.out.println(\\"Hello from Java\\");\\n }\\n}\\n",\n "/private/tmp/docker_tmpkyipo8y7/Hello.java",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 4864f67aab6874db8b656c7b15bd7cfc595e9571 data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nINFO cwltool:job.py:419 [job create-tar] completed success\nDEBUG cwltool:job.py:422 [job create-tar] outputs {\n "tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step create-tar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:572 [step create-tar] completed success\nDEBUG cwltool:job.py:446 [job create-tar] Removing input staging directory /private/tmp/docker_tmpzx57hfi5\nDEBUG cwltool:job.py:454 [job create-tar] Removing temporary directory /private/tmp/docker_tmp4rtd4n2g\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step compile\nDEBUG cwltool:workflow_job.py:727 [step compile] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step compile] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step compile] start\nDEBUG cwltool:workflow_job.py:498 [workflow compile] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow compile] start\nDEBUG cwltool:workflow_job.py:777 [workflow compile] inputs {\n "ex": "Hello.java",\n "inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:610 [workflow compile] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument not ready\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step untar\nDEBUG cwltool:workflow_job.py:727 [step untar] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step untar] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step untar] start\nDEBUG cwltool:command_line_tool.py:982 [job untar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/tar-param.cwl as part of step untar\nDEBUG cwltool:command_line_tool.py:988 [job untar] {\n "extractfile": "Hello.java",\n "tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job untar] path mappings is {\n "file:///private/tmp/docker_tmpkyipo8y7/hello.tar": [\n "/private/tmp/docker_tmpkyipo8y7/hello.tar",\n "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job untar] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "tar"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "xf"\n },\n {\n "position": [\n 1,\n "tarfile"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9",\n "path": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "dirname": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134"\n }\n },\n {\n "position": [\n 2,\n "extractfile"\n ],\n "datum": "Hello.java"\n }\n]\nDEBUG cwltool:job.py:215 [job untar] initial work dir {}\nINFO cwltool:job.py:266 [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 93035905e94e150874f5a881d39f3c5c6378dd38 data/93/93035905e94e150874f5a881d39f3c5c6378dd38\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nINFO cwltool:job.py:419 [job untar] completed success\nDEBUG cwltool:job.py:422 [job untar] outputs {\n "example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step untar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step untar] completed success\nDEBUG cwltool:job.py:446 [job untar] Removing input staging directory /private/tmp/docker_tmp8uve11w8\nDEBUG cwltool:job.py:454 [job untar] Removing temporary directory /private/tmp/docker_tmpnpvtosz9\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step argument\nDEBUG cwltool:workflow_job.py:727 [step argument] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step argument] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:75 [step argument] start\nDEBUG cwltool:command_line_tool.py:982 [job argument] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/arguments.cwl as part of step argument\nDEBUG cwltool:command_line_tool.py:988 [job argument] {\n "src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job argument] path mappings is {\n "file:///private/tmp/docker_tmpc_ieg46p/Hello.java": [\n "/private/tmp/docker_tmpc_ieg46p/Hello.java",\n "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job argument] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "javac"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-d"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(runtime.outdir)"\n },\n {\n "position": [\n 1,\n "src"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5",\n "path": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "dirname": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/openjdk:9.0.1-11-slim\']\nDEBUG cwltool:job.py:215 [job argument] initial work dir {}\nINFO cwltool:job.py:266 [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\nINFO cwltool:job.py:905 [job argument] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 39e3219327347c05aa3e82236f83aa6d77fe6bfd data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nINFO cwltool:job.py:419 [job argument] completed success\nDEBUG cwltool:job.py:422 [job argument] outputs {\n "classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step argument] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step argument] completed success\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 83049fca7761d12fb0a5da48da3c037c5304a0fc metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 60258aab9b1b640774e4705795ed3f7ae538c98238f3fae97911d4b93bbfaa2d metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 33139ea057934520ce5f2525af14fafb879322770000acdb150ee5aa445568f3588850a5f5951dce7a03937af0e4ae1ecddafaff17b8299b4e9b2d2372aa07e7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0304d4e8c149fbe870496f20f4c073b6946f7fe7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 13120ba16180324a0c690989fede01b2424adce87145cd0da6492b177f8f814c metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 86e81f57bbb1e5335d9dd2921076dfeba39e953bc4214261e7d818a3a7f38ebb9c4367320cf6fa2714c96e00132009d102c6b6604f36fefc1639cdb722d70715 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: cff4ad2216ea628f4975c69699c8e3fc0c3e4632 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 5d742295d8aba73c67424e366c394e0a34f773985c1645c9b6910e35e353afc9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c6b20c2741a3fa0edeb70054d7f72885b90dd62331b41d5f9fb9f2032495d78b83428995111a6ba52d098f57d976c760321811e6ea182d2e2f562976ba5ad1c9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 1fdf97a3b214d0a050db07a554ecfe44b056e655 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 325d75d9f711a5a12feee43188da250d5fdc200b6ca2e33214209fed193a87c8 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8cac58c921bd6a7115ef1dace866bdb2b84dd948cbed5014ab70eae79abe7b30e8ddeafc033659ddb581ac53550230aa818e3623fc55cebae094df17b7b9cd64 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9f2ad16a37a1df641dfe180c8704e88211c46676 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 939e5a54c9079007e36c852408057047622c11cb1d06b2b64b82636d8a1d6762 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 65707a62469cf55e9dcb8fdfe87bf1af958df3846a5de0a6c4732557af5ad6ddfd07fae87e80e7c4c3cef36d0b3b25b03293a5805ddeecf1d86980a7bff1e885 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9be8dfc973c5248324d388bda772ced2eafc5d09 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 4ad66e5bea19ad398ad45267244c6fb7e950340d509df851edbad2fbb844a504 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 63e5b105c46bef759931359c5994f6cff8029bb8a59911a3458df8d1e4e1b98fb3b6f8689c2096670880e2833bd3ae7e369b8e77ef0c7ae613edb86ff6dd9887 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nINFO cwltool:workflow_job.py:539 [workflow compile] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow compile] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step compile] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step compile] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:job.py:446 [job argument] Removing input staging directory /private/tmp/docker_tmpebe5z0v8\nDEBUG cwltool:job.py:454 [job argument] Removing temporary directory /private/tmp/docker_tmpdff4tkfu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpepzg_f_c/Hello.class to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzrpr1a4o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr_sgrnnb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpepzg_f_c\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkyipo8y7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpc_ieg46p\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 19fbff09cc97d57d7241305ed0cb03212f211ae9 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 410b6c9c1c10cc229c8781ddc5074f25f371cdf9b4e6e053758e98931db2f7eb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 6c75e7c3ef6bf96b917b3961bf1350658fec598fb67d194716c7fa281d09ae834cf81cea64f8636e34b2a8391b8d4391e267b526d90b3460ed50ffa35b615b9f metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 42906be32350038218f034e2418bfa414323fecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 54d1a6a2ea333664645b1ef510288b473b2798d0eba102c7d9f83979acdb30ea metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 59de6004ed6286c5bf4461690f1eea3eecec94be8cf7f186aa9100dd447ed2d3f8e78d8bb9a09b712d6bf0c16f036559fb76f2e57f9c9bf47f5b868d5a5b1698 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 54936279704d89dd038e6bb6207276b94ccf52c7 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48a6d44504c674c65ae71bf0186c051343568e8b1796272af0adf58b39dfc015 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 77323c4d9ca07d91bcb9db9f7090422963c30ec31c9cc7312a2619f60dfb0f8632630019a19f57fd3f2bbe2a354d0328dfb60c482f81141a31ea1b3c118e2466 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 76273be200ec2c229e213509b9bb670478dce7f4 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48244946e314f094d1b6c4b6e30a3358b5cbca006e442806c064eb0ffb961c1a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 64a2901aa5304fa5d65408f3a61b12c9131f251d89f4e688f9c3c3cdcba700f7fc67069606af5b24e6196f60e2553a53f51fda4ff970d89a7d91881ff5ffc4b5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: d80b34fd80aa3f9137314feb7021908e2b52cb91 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cc95cb90e86609a55c17cd318a3e5bd9892687cc6df9ba66fc8479dfd0d95aef metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 697c8c7b70137288a5672502d3786e77f04ce6f28f5a549ac71edb9f8bac64d7cb6ee4ef13ce84d9184f865db3ccaa66cf20bc62f31824e4b558a9bb959d6ef4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: f8b1b468869ac1a80043e092868c2277f1d15c64 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1805212079569e9a572fab9cdb3b73665e98e5ca3ec88d9b637ee30ffd026e11 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 036d8f071535a67857917407770951d720c444f3b9057b0bd8194be89066977bcc223f1ad268b552ea07d143c886679c4cbb66d79a0dea214672d54ec41358ff metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'classout\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello.class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 419\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a77f1bf715803e410ab8646eec4bee4f620aca8f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 023017d52b11f799321c82c33eb3f4b053ed57872618d37d30b69ec0c64902f8 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8e911b78c78b0a5146fc24f8adbdf1f253a2d78f6239c81533b0166ebd4f7ed7dd64e7fb3f86a7f62eb6d4288ade648629ef6c28ad1ab4accadc2800a8038123 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 724b068a51d129c5492f28865b3bed0eb22a8dec snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 0727286ce68bebcae06f0cb1da28a58382c9db14f0e4eae7e29f5644483d16cb snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c116c653cd68a7fd934d7df77d24a4977efa1c6505d6c32b138aec44130d40228f7d69bf3b11fb9473e421755e7d592f15b1aa93c988b1ec3249dc84139b7960 snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 7b997f5397fd668969634a4e8c113cec0fbbc5e8 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cdd580b6c0f37c60cc39ef4968184235ade6ab7369329b363c5db7f101f6d3a4 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 3c72796915141289f4e94ec0b83fa5fbd0203d8afb69adf0dcd866a616ddc9a432d071e75e54f3eafcd3d850411b6cfb54643cf123fb246206f49885a0b5fdbf snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b9b609b8713bd5ebed4e83e8074f84648a5f6708 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 6ddc89e25e65a9a6e80de48be06442cef0128b9f1c82ec8d50019223c5bfd866 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 58e44c861533f86faee277fc618bd869781ec5c1203bad37d150dd5efaed44d51198c9fed40ddd62b9ef348e2a9b9f5004d86c9983ee22ac61070b0c588a8229 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a11e6ae3b6824babd50ca5a96395030d203565f6 snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ba73050af0d17a6a24d82aeb88b54150e38189056007f1dd094a59562f30475d snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 57fe970c776bf2b8f283783b6565d886acd7f5974ec7a7a9de547201585a93130c40b494e29bb2a489123dc5d0c30f791c585f1f29dc11ff8d381b16c7d9e348 snapshot/tar-param.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0dd82b60f74970af2204ec209f5d9ba9bcf90ab1 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1991adaba7d0cdd01efb884f896e70162a678d6c019c8af40a628e3e81c958dd metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c8b1f27a515fda5fffc55d93abf31ae91d00fe9077046e16109522c83fd5740e4df390bb7dce1e8d7c5ee00e3d1532e298ee248addec8623f2d88f1f0b5d94d4 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b201b1900b531a5cac833222efcf2ea148ee8e4f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: be90e3007275188cbc913e1d8e0b2901a70917ecb0c4d82a9967a894ad18fc33 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca20cd4c002dea5a664c54c7a7d874ed07461ed50baf0016e4e9c45fdaa16132772748146c0f39bf409004e80e3c2ee9db16490543e86a8e41e45cea5758d3af metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 8e62f08782410be5f7a325ad891118c1c8b048c9 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: af35cf1992cf37219396ab2b24f2c0bc89e1e9d3fa27c63d3f8c8a2a64c2b62a bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c3bdb2ec78cc257d15b637073d81804b259e9bd197b9b0aa71d9a3b66b7eee0df29dbd0f6146ebdb9fee6e3adc073a09a3cd260708cc7890a982c547bb28d165 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance')] + duration: 5.002003371999308 + start: 1685951459.705703 + stop: 1685951464.707586 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_nested_workflow + location: ('tests/test_provenance.py', 98, 'test_nested_workflow') + keywords: {'test_nested_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "classout": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class",\n "basename": "Hello.class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _18] start\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step create-tar\n\x1b[1;30mINFO\x1b[0m [step create-tar] start\n\x1b[1;30mINFO\x1b[0m [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nMon Jun 5 09:51:00 CEST 2023\nMon Jun 5 09:51:00 CEST 2023\n\x1b[1;30mINFO\x1b[0m [job create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [step create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step compile\n\x1b[1;30mINFO\x1b[0m [step compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step untar\n\x1b[1;30mINFO\x1b[0m [step untar] start\n\x1b[1;30mINFO\x1b[0m [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\n\x1b[1;30mINFO\x1b[0m [job untar] completed success\n\x1b[1;30mINFO\x1b[0m [step untar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step argument\n\x1b[1;30mINFO\x1b[0m [step argument] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/openjdk:9.0.1-11-slim']\n9.0.1-11-slim: Pulling from library/openjdk\nDigest: sha256:dc239c9a17aa509d4e79dc4980e40a5f0c8af78a9bcefab2b5eedf819f702298\nStatus: Image is up to date for openjdk:9.0.1-11-slim\ndocker.io/library/openjdk:9.0.1-11-slim\n\x1b[1;30mINFO\x1b[0m [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\n\x1b[1;30mINFO\x1b[0m [job argument] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job argument] completed success\n\x1b[1;30mINFO\x1b[0m [step argument] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] completed success\n\x1b[1;30mINFO\x1b[0m [step compile] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 74ece951469a5306ac6512cff2a9f3b25b91c858 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: a0f6fb34d0ba97018b294486569ded02bb6e6e659d3e06c5de4f214582691f36 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: f0dca2f20d6e9cd7b5ca6e9ea53e3c5548164e2b77ca0b2a1f3e785ce12f314ca29d1943f80ee974373ab7ead0031aee08c07bb511c34c82cc951e3bef28c9b0 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _18] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile not ready\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step create-tar\nDEBUG cwltool:workflow_job.py:727 [step create-tar] job input {}\nDEBUG cwltool:workflow_job.py:732 [step create-tar] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step create-tar] start\nDEBUG cwltool:command_line_tool.py:982 [job create-tar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/fbd87079-fe0c-4de9-b99f-0c79323cf2c1 as part of step create-tar\nDEBUG cwltool:command_line_tool.py:988 [job create-tar] {}\nDEBUG cwltool:command_line_tool.py:1000 [job create-tar] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job create-tar] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "date\\ntar cf hello.tar Hello.java\\ndate\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job create-tar] initial work dir {\n "_:5de9498b-d23e-4bbf-b5e6-3d9459eedb80": [\n "public class Hello {\\n public static void main(String[] argv) {\\n System.out.println(\\"Hello from Java\\");\\n }\\n}\\n",\n "/private/tmp/docker_tmpkyipo8y7/Hello.java",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 4864f67aab6874db8b656c7b15bd7cfc595e9571 data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nINFO cwltool:job.py:419 [job create-tar] completed success\nDEBUG cwltool:job.py:422 [job create-tar] outputs {\n "tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step create-tar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:572 [step create-tar] completed success\nDEBUG cwltool:job.py:446 [job create-tar] Removing input staging directory /private/tmp/docker_tmpzx57hfi5\nDEBUG cwltool:job.py:454 [job create-tar] Removing temporary directory /private/tmp/docker_tmp4rtd4n2g\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step compile\nDEBUG cwltool:workflow_job.py:727 [step compile] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step compile] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step compile] start\nDEBUG cwltool:workflow_job.py:498 [workflow compile] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow compile] start\nDEBUG cwltool:workflow_job.py:777 [workflow compile] inputs {\n "ex": "Hello.java",\n "inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:610 [workflow compile] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument not ready\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step untar\nDEBUG cwltool:workflow_job.py:727 [step untar] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step untar] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step untar] start\nDEBUG cwltool:command_line_tool.py:982 [job untar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/tar-param.cwl as part of step untar\nDEBUG cwltool:command_line_tool.py:988 [job untar] {\n "extractfile": "Hello.java",\n "tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job untar] path mappings is {\n "file:///private/tmp/docker_tmpkyipo8y7/hello.tar": [\n "/private/tmp/docker_tmpkyipo8y7/hello.tar",\n "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job untar] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "tar"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "xf"\n },\n {\n "position": [\n 1,\n "tarfile"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9",\n "path": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "dirname": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134"\n }\n },\n {\n "position": [\n 2,\n "extractfile"\n ],\n "datum": "Hello.java"\n }\n]\nDEBUG cwltool:job.py:215 [job untar] initial work dir {}\nINFO cwltool:job.py:266 [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 93035905e94e150874f5a881d39f3c5c6378dd38 data/93/93035905e94e150874f5a881d39f3c5c6378dd38\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nINFO cwltool:job.py:419 [job untar] completed success\nDEBUG cwltool:job.py:422 [job untar] outputs {\n "example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step untar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step untar] completed success\nDEBUG cwltool:job.py:446 [job untar] Removing input staging directory /private/tmp/docker_tmp8uve11w8\nDEBUG cwltool:job.py:454 [job untar] Removing temporary directory /private/tmp/docker_tmpnpvtosz9\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step argument\nDEBUG cwltool:workflow_job.py:727 [step argument] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step argument] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:75 [step argument] start\nDEBUG cwltool:command_line_tool.py:982 [job argument] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/arguments.cwl as part of step argument\nDEBUG cwltool:command_line_tool.py:988 [job argument] {\n "src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job argument] path mappings is {\n "file:///private/tmp/docker_tmpc_ieg46p/Hello.java": [\n "/private/tmp/docker_tmpc_ieg46p/Hello.java",\n "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job argument] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "javac"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-d"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(runtime.outdir)"\n },\n {\n "position": [\n 1,\n "src"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5",\n "path": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "dirname": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/openjdk:9.0.1-11-slim\']\nDEBUG cwltool:job.py:215 [job argument] initial work dir {}\nINFO cwltool:job.py:266 [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\nINFO cwltool:job.py:905 [job argument] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 39e3219327347c05aa3e82236f83aa6d77fe6bfd data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nINFO cwltool:job.py:419 [job argument] completed success\nDEBUG cwltool:job.py:422 [job argument] outputs {\n "classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step argument] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step argument] completed success\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 83049fca7761d12fb0a5da48da3c037c5304a0fc metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 60258aab9b1b640774e4705795ed3f7ae538c98238f3fae97911d4b93bbfaa2d metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 33139ea057934520ce5f2525af14fafb879322770000acdb150ee5aa445568f3588850a5f5951dce7a03937af0e4ae1ecddafaff17b8299b4e9b2d2372aa07e7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0304d4e8c149fbe870496f20f4c073b6946f7fe7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 13120ba16180324a0c690989fede01b2424adce87145cd0da6492b177f8f814c metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 86e81f57bbb1e5335d9dd2921076dfeba39e953bc4214261e7d818a3a7f38ebb9c4367320cf6fa2714c96e00132009d102c6b6604f36fefc1639cdb722d70715 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: cff4ad2216ea628f4975c69699c8e3fc0c3e4632 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 5d742295d8aba73c67424e366c394e0a34f773985c1645c9b6910e35e353afc9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c6b20c2741a3fa0edeb70054d7f72885b90dd62331b41d5f9fb9f2032495d78b83428995111a6ba52d098f57d976c760321811e6ea182d2e2f562976ba5ad1c9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 1fdf97a3b214d0a050db07a554ecfe44b056e655 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 325d75d9f711a5a12feee43188da250d5fdc200b6ca2e33214209fed193a87c8 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8cac58c921bd6a7115ef1dace866bdb2b84dd948cbed5014ab70eae79abe7b30e8ddeafc033659ddb581ac53550230aa818e3623fc55cebae094df17b7b9cd64 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9f2ad16a37a1df641dfe180c8704e88211c46676 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 939e5a54c9079007e36c852408057047622c11cb1d06b2b64b82636d8a1d6762 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 65707a62469cf55e9dcb8fdfe87bf1af958df3846a5de0a6c4732557af5ad6ddfd07fae87e80e7c4c3cef36d0b3b25b03293a5805ddeecf1d86980a7bff1e885 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9be8dfc973c5248324d388bda772ced2eafc5d09 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 4ad66e5bea19ad398ad45267244c6fb7e950340d509df851edbad2fbb844a504 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 63e5b105c46bef759931359c5994f6cff8029bb8a59911a3458df8d1e4e1b98fb3b6f8689c2096670880e2833bd3ae7e369b8e77ef0c7ae613edb86ff6dd9887 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nINFO cwltool:workflow_job.py:539 [workflow compile] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow compile] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step compile] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step compile] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:job.py:446 [job argument] Removing input staging directory /private/tmp/docker_tmpebe5z0v8\nDEBUG cwltool:job.py:454 [job argument] Removing temporary directory /private/tmp/docker_tmpdff4tkfu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpepzg_f_c/Hello.class to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzrpr1a4o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr_sgrnnb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpepzg_f_c\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkyipo8y7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpc_ieg46p\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 19fbff09cc97d57d7241305ed0cb03212f211ae9 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 410b6c9c1c10cc229c8781ddc5074f25f371cdf9b4e6e053758e98931db2f7eb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 6c75e7c3ef6bf96b917b3961bf1350658fec598fb67d194716c7fa281d09ae834cf81cea64f8636e34b2a8391b8d4391e267b526d90b3460ed50ffa35b615b9f metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 42906be32350038218f034e2418bfa414323fecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 54d1a6a2ea333664645b1ef510288b473b2798d0eba102c7d9f83979acdb30ea metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 59de6004ed6286c5bf4461690f1eea3eecec94be8cf7f186aa9100dd447ed2d3f8e78d8bb9a09b712d6bf0c16f036559fb76f2e57f9c9bf47f5b868d5a5b1698 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 54936279704d89dd038e6bb6207276b94ccf52c7 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48a6d44504c674c65ae71bf0186c051343568e8b1796272af0adf58b39dfc015 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 77323c4d9ca07d91bcb9db9f7090422963c30ec31c9cc7312a2619f60dfb0f8632630019a19f57fd3f2bbe2a354d0328dfb60c482f81141a31ea1b3c118e2466 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 76273be200ec2c229e213509b9bb670478dce7f4 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48244946e314f094d1b6c4b6e30a3358b5cbca006e442806c064eb0ffb961c1a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 64a2901aa5304fa5d65408f3a61b12c9131f251d89f4e688f9c3c3cdcba700f7fc67069606af5b24e6196f60e2553a53f51fda4ff970d89a7d91881ff5ffc4b5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: d80b34fd80aa3f9137314feb7021908e2b52cb91 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cc95cb90e86609a55c17cd318a3e5bd9892687cc6df9ba66fc8479dfd0d95aef metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 697c8c7b70137288a5672502d3786e77f04ce6f28f5a549ac71edb9f8bac64d7cb6ee4ef13ce84d9184f865db3ccaa66cf20bc62f31824e4b558a9bb959d6ef4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: f8b1b468869ac1a80043e092868c2277f1d15c64 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1805212079569e9a572fab9cdb3b73665e98e5ca3ec88d9b637ee30ffd026e11 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 036d8f071535a67857917407770951d720c444f3b9057b0bd8194be89066977bcc223f1ad268b552ea07d143c886679c4cbb66d79a0dea214672d54ec41358ff metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'classout\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello.class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 419\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a77f1bf715803e410ab8646eec4bee4f620aca8f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 023017d52b11f799321c82c33eb3f4b053ed57872618d37d30b69ec0c64902f8 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8e911b78c78b0a5146fc24f8adbdf1f253a2d78f6239c81533b0166ebd4f7ed7dd64e7fb3f86a7f62eb6d4288ade648629ef6c28ad1ab4accadc2800a8038123 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 724b068a51d129c5492f28865b3bed0eb22a8dec snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 0727286ce68bebcae06f0cb1da28a58382c9db14f0e4eae7e29f5644483d16cb snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c116c653cd68a7fd934d7df77d24a4977efa1c6505d6c32b138aec44130d40228f7d69bf3b11fb9473e421755e7d592f15b1aa93c988b1ec3249dc84139b7960 snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 7b997f5397fd668969634a4e8c113cec0fbbc5e8 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cdd580b6c0f37c60cc39ef4968184235ade6ab7369329b363c5db7f101f6d3a4 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 3c72796915141289f4e94ec0b83fa5fbd0203d8afb69adf0dcd866a616ddc9a432d071e75e54f3eafcd3d850411b6cfb54643cf123fb246206f49885a0b5fdbf snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b9b609b8713bd5ebed4e83e8074f84648a5f6708 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 6ddc89e25e65a9a6e80de48be06442cef0128b9f1c82ec8d50019223c5bfd866 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 58e44c861533f86faee277fc618bd869781ec5c1203bad37d150dd5efaed44d51198c9fed40ddd62b9ef348e2a9b9f5004d86c9983ee22ac61070b0c588a8229 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a11e6ae3b6824babd50ca5a96395030d203565f6 snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ba73050af0d17a6a24d82aeb88b54150e38189056007f1dd094a59562f30475d snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 57fe970c776bf2b8f283783b6565d886acd7f5974ec7a7a9de547201585a93130c40b494e29bb2a489123dc5d0c30f791c585f1f29dc11ff8d381b16c7d9e348 snapshot/tar-param.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0dd82b60f74970af2204ec209f5d9ba9bcf90ab1 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1991adaba7d0cdd01efb884f896e70162a678d6c019c8af40a628e3e81c958dd metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c8b1f27a515fda5fffc55d93abf31ae91d00fe9077046e16109522c83fd5740e4df390bb7dce1e8d7c5ee00e3d1532e298ee248addec8623f2d88f1f0b5d94d4 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b201b1900b531a5cac833222efcf2ea148ee8e4f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: be90e3007275188cbc913e1d8e0b2901a70917ecb0c4d82a9967a894ad18fc33 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca20cd4c002dea5a664c54c7a7d874ed07461ed50baf0016e4e9c45fdaa16132772748146c0f39bf409004e80e3c2ee9db16490543e86a8e41e45cea5758d3af metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 8e62f08782410be5f7a325ad891118c1c8b048c9 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: af35cf1992cf37219396ab2b24f2c0bc89e1e9d3fa27c63d3f8c8a2a64c2b62a bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c3bdb2ec78cc257d15b637073d81804b259e9bd197b9b0aa71d9a3b66b7eee0df29dbd0f6146ebdb9fee6e3adc073a09a3cd260708cc7890a982c547bb28d165 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance')] + duration: 0.00113051800053654 + start: 1685951464.710773 + stop: 1685951464.711905 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_nested_workflow + location: ('tests/test_provenance.py', 98, 'test_nested_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + nodeid: tests/test_provenance.py::test_nested_workflow + when: runtest + location: None + finish pytest_warning_recorded --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_secondary_files_implicit + location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_secondary_files_implicit + location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') + keywords: {'test_secondary_files_implicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0012492460000430583 + start: 1685951464.7161531 + stop: 1685951464.717403 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + early skip of rewriting module: encodings.ascii [assertion] + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_secondary_files_implicit + location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') + keywords: {'test_secondary_files_implicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'--file1\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7fbe1688c021dd47067816cb1915f194a21b192a workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: fdd353f2fc1a5ce060db48433d4c5d39841c3a16a7b3859ecf40c5d0559585cb workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5af67683ddcf0dc25317f9299432e1b480cba92fefc530bb82144c0b46d090163964253480d1d2b57d8d93bc800be27c6a17552dff8d5d285dfea3792633143a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx",\n "size": 3\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpwlagwb74\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpneari7wr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmprjpz3kex\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm23vbaqp\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b4bef5453619901d1f8f99b5ae6de84b0d9e639b metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 5db39cc34f5ff26b64a03b03b9101fecc2312db65289fe2d1be735727992d8bd metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 8d283d305c0e6d11608b05d9a5e1ba5a75fb4aba75402c34b62e6d7daa1524e3e4995c7b5b7dd09e2e1b461a78c125bc27d82023ed600a5efe3ca285ad10ea97 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 8727ee5875ce1f873aaea8acd610451c6f552485 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 7ea7c1f314778c5b956cac5c77bce95ea6b88611ebbc7066030f869d1db4451d metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: bfc8b1282a1fb06945d4fe7918b05d4f0406bbf7cb97de9e7fc3a34a9d24662816b96a4494d9a1063a86717119f908eb3bf90fe45fe4ef1c346c31b9266615c3 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 137c02dbe6b251a0db3df717988e236021b8999b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 563c5a34f521209ac347f8053149f64041ee7b452c394b4d8c04be39be52d09c metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 2eb1f8f6df902d2db5dab2f042daad6a2b591ba84f6017b4920c49d9a72328f2c0e3b8624a9d3b4740645ab3df6fcbfea29f90b796df9be09a37cf9d455769dc metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: f958ba8327cc8b9af11b209e763c08fd828c4aae metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9eee73bac677248e20e3fdc1b3945afaa24f84f31779a432ecc800f5959ac994 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 98aff7bc546d9f42dfcb7cfc86031061cd09819e93cafb46dea0818f5f55023540eed22292a07e8cbee2e3b5a0a3da1b5096d16a38d308112c5b359c4a7e66ef metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 28ac6c4bb8ee879415c09c5c428f9e146863163b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd2b49ac8dce047e8c28351499fefd31d5acd14bd37d5bbb2a984b091accd35d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5a11c7149e3fe38c8365859626f63e90a4a2edbd1603d17ab341ef329bbe5a0b5408df2f612212175eec6fef219878b2cd631e8924ff2f66fab9df76f87a5d2b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 52e03863abba9f946950a2419bc5a3c9d593fd04 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 8e79daf03e3958103d27e310d0879c8812989df38d007346f55fb9433c4108c8 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 00f022778fd2a8b71a936a2bb5b382645d9663735588b29c3a4228989d43026867c3654b71a7087b9bdd09ebcdf95d5e97d22cabef6d0404bff05a436c15996b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 4b5fce360bf0db096420ddf360cb05fb63abef9a metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 12c59130a589553031e8a732559d20225da263aa19d2b43b4f23f2ff47a13396 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: a0f2b7ecf70b39b1e7b84ddab845455bf81f04019ecf1810b9540809be18cfb5a5fcdeb90986c4b11d0d86c85d38ced387beb5248a97e75460019687346cca41 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7da08c3bcf057f5790aae85a316cc4c7e84e8dae metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9822a8bb8f23ff4a5f546df0e1901dac8ce404c90cc9e864c932e858f342296c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 20961f19fd0db8bf533ce8aa98d561c15d672364183fc007e488c01e40271698363b6d1e35edfd4d109b9863391b666e44cb49cbec572343804ee8aec795de28 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3a83e9297c5eca6e6de723837360f84464d4ee94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 57f04fd3cbd44703b65a45ec0acd6b1e56243dd599476dff375f2c868198939d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 7eca04aa9b2734f1b61e65c7f009cd6ddd45735a0c303dd0653b766f411e9fdea1255c5db384dd0b3f787f5b1920fbacdea475948ad439ac70e2589a09f42b46 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance')] + duration: 1.082738922000317 + start: 1685951464.7178009 + stop: 1685951465.800514 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_secondary_files_implicit + location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') + keywords: {'test_secondary_files_implicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'--file1\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7fbe1688c021dd47067816cb1915f194a21b192a workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: fdd353f2fc1a5ce060db48433d4c5d39841c3a16a7b3859ecf40c5d0559585cb workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5af67683ddcf0dc25317f9299432e1b480cba92fefc530bb82144c0b46d090163964253480d1d2b57d8d93bc800be27c6a17552dff8d5d285dfea3792633143a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx",\n "size": 3\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpwlagwb74\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpneari7wr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmprjpz3kex\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm23vbaqp\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b4bef5453619901d1f8f99b5ae6de84b0d9e639b metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 5db39cc34f5ff26b64a03b03b9101fecc2312db65289fe2d1be735727992d8bd metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 8d283d305c0e6d11608b05d9a5e1ba5a75fb4aba75402c34b62e6d7daa1524e3e4995c7b5b7dd09e2e1b461a78c125bc27d82023ed600a5efe3ca285ad10ea97 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 8727ee5875ce1f873aaea8acd610451c6f552485 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 7ea7c1f314778c5b956cac5c77bce95ea6b88611ebbc7066030f869d1db4451d metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: bfc8b1282a1fb06945d4fe7918b05d4f0406bbf7cb97de9e7fc3a34a9d24662816b96a4494d9a1063a86717119f908eb3bf90fe45fe4ef1c346c31b9266615c3 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 137c02dbe6b251a0db3df717988e236021b8999b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 563c5a34f521209ac347f8053149f64041ee7b452c394b4d8c04be39be52d09c metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 2eb1f8f6df902d2db5dab2f042daad6a2b591ba84f6017b4920c49d9a72328f2c0e3b8624a9d3b4740645ab3df6fcbfea29f90b796df9be09a37cf9d455769dc metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: f958ba8327cc8b9af11b209e763c08fd828c4aae metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9eee73bac677248e20e3fdc1b3945afaa24f84f31779a432ecc800f5959ac994 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 98aff7bc546d9f42dfcb7cfc86031061cd09819e93cafb46dea0818f5f55023540eed22292a07e8cbee2e3b5a0a3da1b5096d16a38d308112c5b359c4a7e66ef metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 28ac6c4bb8ee879415c09c5c428f9e146863163b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd2b49ac8dce047e8c28351499fefd31d5acd14bd37d5bbb2a984b091accd35d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5a11c7149e3fe38c8365859626f63e90a4a2edbd1603d17ab341ef329bbe5a0b5408df2f612212175eec6fef219878b2cd631e8924ff2f66fab9df76f87a5d2b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 52e03863abba9f946950a2419bc5a3c9d593fd04 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 8e79daf03e3958103d27e310d0879c8812989df38d007346f55fb9433c4108c8 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 00f022778fd2a8b71a936a2bb5b382645d9663735588b29c3a4228989d43026867c3654b71a7087b9bdd09ebcdf95d5e97d22cabef6d0404bff05a436c15996b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 4b5fce360bf0db096420ddf360cb05fb63abef9a metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 12c59130a589553031e8a732559d20225da263aa19d2b43b4f23f2ff47a13396 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: a0f2b7ecf70b39b1e7b84ddab845455bf81f04019ecf1810b9540809be18cfb5a5fcdeb90986c4b11d0d86c85d38ced387beb5248a97e75460019687346cca41 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7da08c3bcf057f5790aae85a316cc4c7e84e8dae metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9822a8bb8f23ff4a5f546df0e1901dac8ce404c90cc9e864c932e858f342296c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 20961f19fd0db8bf533ce8aa98d561c15d672364183fc007e488c01e40271698363b6d1e35edfd4d109b9863391b666e44cb49cbec572343804ee8aec795de28 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3a83e9297c5eca6e6de723837360f84464d4ee94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 57f04fd3cbd44703b65a45ec0acd6b1e56243dd599476dff375f2c868198939d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 7eca04aa9b2734f1b61e65c7f009cd6ddd45735a0c303dd0653b766f411e9fdea1255c5db384dd0b3f787f5b1920fbacdea475948ad439ac70e2589a09f42b46 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance')] + duration: 0.0008646879996376811 + start: 1685951465.802495 + stop: 1685951465.803361 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_secondary_files_implicit + location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + nodeid: tests/test_provenance.py::test_secondary_files_implicit + when: runtest + location: None + finish pytest_warning_recorded --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_secondary_files_explicit + location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_secondary_files_explicit + location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') + keywords: {'test_secondary_files_explicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.022172081999997317 + start: 1685951465.808274 + stop: 1685951465.8304498 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_secondary_files_explicit + location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') + keywords: {'test_secondary_files_explicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\n\x1b[1;30mINFO\x1b[0m [workflow _20] start\n\x1b[1;30mINFO\x1b[0m [workflow _20] starting step step1_4\n\x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[1;30mINFO\x1b[0m [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\n\x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _20] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ab5d55af482cae1b1829c3da3ee604ee1fb46e6c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: e16b2b9f3a4ea3c4db3ad2bb71e39cdd02c1fde2a446528a68596c88de6ce0ad workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0173fb349bad74105b30c7b54ebfc79bc650689ee08d2810530ae536a1b064eaf25c7b9f15d9c9dfd3e685437e64a2e8d5c55dd9ac21dae1ac0ee2dc95b3c641 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmp9gj9l2fa\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp46c_retm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5ft4gx95\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp96w7gil\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 509e405f0bd8ef93211df57e39be176d12666adc metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 262ec7432d66db0b5ed1cd59aa1af4cd4be1124dbc4af94e86bb6b512289b670 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0119a8de57eb87221919bb6f241bdbe06282b70055adb1d5ae33b9c6f69d081928b3f227305cef219b208ab543d013f5244e55ec7b86517988eaed08f44786f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 45b1c340c57cf230ed17b4e630abdf1efade240e metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: eb6898093916925d311c393e4d05c7526bb1cc611d0dde25b34dd9e93b53bbc4 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 3bf0f3cd885ac1a11daa3a4ddd0c2a1629c6ca2c4ebbb55721070a7aab577a15e431939a7983d567fdfc52b7c6cd4ac9cc7301dc550254a3f5c54bc614f33337 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 38e4d26d88163d39f1f79746d91c385a30ee9225 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0541fdfe699859ca640f637778cffea97fd5bb4b10fae765cca532bb51594598 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: dd848f7099d65e87f01861744621b13563715b0af772ac3f9c254aaf22da244075483bb03cd153771798371887f6435b579e557f5fc8e0b55abcbd63d11b3671 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0a9161af759436c0940176a0ee92ac46d033a8d2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d975c4b3006cb518b3712877f983b68a2f38e2860b23bbda21d4d5c6bc82482d metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: af800227b8ede5af124ae87add535d60d7565a31b2e0923532a6442d21e755820ef1dee20d54db2aae2585bbdc1f1d566b1a76a4d251b80d6183146da3b14b9c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 6f16628a75ecb5bc263b08aa80b2b04c289f6b85 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d7a309d015efc43f7c0d10319bd7866a9e569b1ceb945c129bfc0108f1baeeb7 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 60585141255cb9b43faafbfa26e49d21ddaeff3718becc211fc229d7b9dc2201ae89245239fc3ff9e03726bd8d99faa864df8eb661810117fb2a43f868188cb3 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0077decebf928c4d8aebf6cd1b9c40ae95443eb6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ccfe9486f117718bb534393411f3535d23abe939688867cd7fb7666948a96040 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 5f7ed9ffdc499c78afe431fa0d3ed7bd2942590ddb4cdb42b728daae7644af1f50f352669a364b61880354e56de96674c7b9faa918f33ebd112dc80f3194aa5a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ecdb0d529e82bcfae2510df67a6c624ec91cb4eb metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: f3498f65cdd7f44b2f46cdc5f8a6630bd922452b6bed63648fd8a0b0636b53e9 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 140511736f43c0e44321a2d677bb2e54684fa8e564d650558381799123517ea7a27402ecf6c826c0651360dbc351f4903847f1dc7552ecbc7bc5f372963395f7 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b73fda4904dd1bea80c96c9fc89e49aabbd83fff metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 9f14d52b82857ac1b7a45eb1bf0f6ee22105533f54c1af788fec3744102e8d97 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: b5c96592dbe7dd23e27053f734d227f91c089e42395a9a812dc4994fce5850b58c7ae04d804f92a0041ed0487a26a4e0011cd626bcd86621ae9cd773d631daae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: a28a0bc657b6e1797cdbfe4343a9adfad7fbc539 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: b32be96d6dc9f72b299be94d867dd45f884d5e0f5c416b98f8f03e691ddecec3 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 6145e7ae857af5949152de4f2773425ea722b736616597d7c4766ad6b85b57435c37240b545b770e500e565af57ba9ae25b498dfaa8c31003b65f066cfb9a62b bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance')] + duration: 1.0753109860006589 + start: 1685951465.8310468 + stop: 1685951466.9063349 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_secondary_files_explicit + location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') + keywords: {'test_secondary_files_explicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\n\x1b[1;30mINFO\x1b[0m [workflow _20] start\n\x1b[1;30mINFO\x1b[0m [workflow _20] starting step step1_4\n\x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[1;30mINFO\x1b[0m [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\n\x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _20] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ab5d55af482cae1b1829c3da3ee604ee1fb46e6c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: e16b2b9f3a4ea3c4db3ad2bb71e39cdd02c1fde2a446528a68596c88de6ce0ad workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0173fb349bad74105b30c7b54ebfc79bc650689ee08d2810530ae536a1b064eaf25c7b9f15d9c9dfd3e685437e64a2e8d5c55dd9ac21dae1ac0ee2dc95b3c641 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmp9gj9l2fa\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp46c_retm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5ft4gx95\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp96w7gil\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 509e405f0bd8ef93211df57e39be176d12666adc metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 262ec7432d66db0b5ed1cd59aa1af4cd4be1124dbc4af94e86bb6b512289b670 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0119a8de57eb87221919bb6f241bdbe06282b70055adb1d5ae33b9c6f69d081928b3f227305cef219b208ab543d013f5244e55ec7b86517988eaed08f44786f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 45b1c340c57cf230ed17b4e630abdf1efade240e metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: eb6898093916925d311c393e4d05c7526bb1cc611d0dde25b34dd9e93b53bbc4 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 3bf0f3cd885ac1a11daa3a4ddd0c2a1629c6ca2c4ebbb55721070a7aab577a15e431939a7983d567fdfc52b7c6cd4ac9cc7301dc550254a3f5c54bc614f33337 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 38e4d26d88163d39f1f79746d91c385a30ee9225 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0541fdfe699859ca640f637778cffea97fd5bb4b10fae765cca532bb51594598 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: dd848f7099d65e87f01861744621b13563715b0af772ac3f9c254aaf22da244075483bb03cd153771798371887f6435b579e557f5fc8e0b55abcbd63d11b3671 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0a9161af759436c0940176a0ee92ac46d033a8d2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d975c4b3006cb518b3712877f983b68a2f38e2860b23bbda21d4d5c6bc82482d metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: af800227b8ede5af124ae87add535d60d7565a31b2e0923532a6442d21e755820ef1dee20d54db2aae2585bbdc1f1d566b1a76a4d251b80d6183146da3b14b9c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 6f16628a75ecb5bc263b08aa80b2b04c289f6b85 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d7a309d015efc43f7c0d10319bd7866a9e569b1ceb945c129bfc0108f1baeeb7 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 60585141255cb9b43faafbfa26e49d21ddaeff3718becc211fc229d7b9dc2201ae89245239fc3ff9e03726bd8d99faa864df8eb661810117fb2a43f868188cb3 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0077decebf928c4d8aebf6cd1b9c40ae95443eb6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ccfe9486f117718bb534393411f3535d23abe939688867cd7fb7666948a96040 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 5f7ed9ffdc499c78afe431fa0d3ed7bd2942590ddb4cdb42b728daae7644af1f50f352669a364b61880354e56de96674c7b9faa918f33ebd112dc80f3194aa5a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ecdb0d529e82bcfae2510df67a6c624ec91cb4eb metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: f3498f65cdd7f44b2f46cdc5f8a6630bd922452b6bed63648fd8a0b0636b53e9 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 140511736f43c0e44321a2d677bb2e54684fa8e564d650558381799123517ea7a27402ecf6c826c0651360dbc351f4903847f1dc7552ecbc7bc5f372963395f7 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b73fda4904dd1bea80c96c9fc89e49aabbd83fff metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 9f14d52b82857ac1b7a45eb1bf0f6ee22105533f54c1af788fec3744102e8d97 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: b5c96592dbe7dd23e27053f734d227f91c089e42395a9a812dc4994fce5850b58c7ae04d804f92a0041ed0487a26a4e0011cd626bcd86621ae9cd773d631daae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: a28a0bc657b6e1797cdbfe4343a9adfad7fbc539 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: b32be96d6dc9f72b299be94d867dd45f884d5e0f5c416b98f8f03e691ddecec3 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 6145e7ae857af5949152de4f2773425ea722b736616597d7c4766ad6b85b57435c37240b545b770e500e565af57ba9ae25b498dfaa8c31003b65f066cfb9a62b bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance')] + duration: 0.0012781379991793074 + start: 1685951466.908513 + stop: 1685951466.9097931 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_secondary_files_explicit + location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + nodeid: tests/test_provenance.py::test_secondary_files_explicit + when: runtest + location: None + finish pytest_warning_recorded --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_dont_require_inputs + location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_dont_require_inputs + location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') + keywords: {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0014646170002379222 + start: 1685951466.91312 + stop: 1685951466.914585 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_dont_require_inputs + location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') + keywords: {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nusage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\n [-h] --input INPUT [job_order]\n/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script: error: the following arguments are required: --input\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 1.982607547999578 + start: 1685951466.914974 + stop: 1685951468.897533 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_dont_require_inputs + location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') + keywords: {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nusage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\n [-h] --input INPUT [job_order]\n/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script: error: the following arguments are required: --input\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.00028186799954710295 + start: 1685951468.898069 + stop: 1685951468.8983521 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_dont_require_inputs + location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: None + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_validate_js_expressions + location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> <_pytest.logging.LogCaptureFixture object at 0x107214a60> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_validate_js_expressions + location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') + keywords: {'test_validate_js_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0003742219996638596 + start: 1685951468.900276 + stop: 1685951468.900651 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_validate_js_expressions + location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') + keywords: {'test_validate_js_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:08]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.\x1b[0m\n"), ('Captured log call', "WARNING cwltool:validate_js.py:208 JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.")] + duration: 0.016739755000344303 + start: 1685951468.9009879 + stop: 1685951468.9177291 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: None + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1043f7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_validate_js_expressions + location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') + keywords: {'test_validate_js_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:08]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.\x1b[0m\n"), ('Captured log call', "WARNING cwltool:validate_js.py:208 JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.")] + duration: 0.0022302220004348783 + start: 1685951468.91821 + stop: 1685951468.920442 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_validate_js_expressions + location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + finish pytest_runtestloop --> True [hook] + pytest_sessionfinish [hook] + session: testsfailed=1 testscollected=664> + exitstatus: 1 + finish pytest_sessionfinish --> [] [hook] + pytest_unconfigure [hook] + config: <_pytest.config.Config object at 0x1043f7730> + finish pytest_unconfigure --> [] [hook] + tests/test_tmpdir.py::test_runtimeContext_respects_tmp_outdir_prefix + location: ('tests/test_tmpdir.py', 253, 'test_runtimeContext_respects_tmp_outdir_prefix') + keywords: {'test_runtimeContext_respects_tmp_outdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.0006812609999542474 + start: 1685951464.2931268 + stop: 1685951464.293809 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_runtimeContext_respects_tmp_outdir_prefix + location: ('tests/test_tmpdir.py', 253, 'test_runtimeContext_respects_tmp_outdir_prefix') + keywords: {'test_runtimeContext_respects_tmp_outdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0003360400005476549 + start: 1685951464.294197 + stop: 1685951464.294534 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_tmpdir.py::test_runtimeContext_respects_tmp_outdir_prefix + location: ('tests/test_tmpdir.py', 253, 'test_runtimeContext_respects_tmp_outdir_prefix') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_tmpdir.py::test_remove_tmpdirs + location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_remove_tmpdirs + location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') + keywords: {'test_remove_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0015675119993829867 + start: 1685951464.296684 + stop: 1685951464.298253 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_remove_tmpdirs + location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') + keywords: {'test_remove_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nHello\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello"\n }\n]\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/2yfuzdes\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/a2i94b9v\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.6808559439996316 + start: 1685951464.298953 + stop: 1685951464.979794 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_remove_tmpdirs + location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') + keywords: {'test_remove_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nHello\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello"\n }\n]\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/2yfuzdes\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/a2i94b9v\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0005884539996259264 + start: 1685951464.980832 + stop: 1685951464.9814222 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_tmpdir.py::test_remove_tmpdirs + location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: ]> + pytest_runtest_logstart [hook] + nodeid: tests/test_tmpdir.py::test_leave_tmpdirs + location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_leave_tmpdirs + location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') + keywords: {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0016575850004301174 + start: 1685951464.983828 + stop: 1685951464.9854872 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_leave_tmpdirs + location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') + keywords: {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env4.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env4.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env4.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env4.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env4.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python3"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "env0.py"\n }\n]\nDEBUG cwltool:job.py:215 [job env4.cwl] initial work dir {\n "_:71d3e5f1-6a63-4f12-8e4e-da560d54b9f0": [\n "import os\\nfor k, v in os.environ.items():\\n print(f\\"{k}={v}\\", end=\\"\\\\0\\")\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/env0.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job env4.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj$ python3 \\\n env0.py > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env4.cwl] completed success\nDEBUG cwltool:job.py:422 [job env4.cwl] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b",\n "basename": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameroot": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6da6366e8e172fcac257989bcfedf15da64e9a2a",\n "size": 1261,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/out/062565172eb482b02386f50adec0303a9a80c77b\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.8227042449998407 + start: 1685951464.986022 + stop: 1685951465.8087091 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: ]> + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_leave_tmpdirs + location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') + keywords: {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env4.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env4.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env4.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env4.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env4.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python3"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "env0.py"\n }\n]\nDEBUG cwltool:job.py:215 [job env4.cwl] initial work dir {\n "_:71d3e5f1-6a63-4f12-8e4e-da560d54b9f0": [\n "import os\\nfor k, v in os.environ.items():\\n print(f\\"{k}={v}\\", end=\\"\\\\0\\")\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/env0.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job env4.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj$ python3 \\\n env0.py > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env4.cwl] completed success\nDEBUG cwltool:job.py:422 [job env4.cwl] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b",\n "basename": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameroot": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6da6366e8e172fcac257989bcfedf15da64e9a2a",\n "size": 1261,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/out/062565172eb482b02386f50adec0303a9a80c77b\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.019946255999457208 + start: 1685951465.809982 + stop: 1685951465.82993 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_tmpdir.py::test_leave_tmpdirs + location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: ]> + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: ]> + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> help with c [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: ExpressionTool + +inputs: + foo: + type: + type: record + fields: + one: File + two: string + +expression: $(inputs.foo.two) + +outputs: [] + [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + finish pytest_fixture_setup --> at 0x10b9b5cf0> [hook] + pytest_fixture_setup [hook] + fixturedef: + request: ]>> + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: ]' when='setup' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0019066180002482724 + start: 1685951465.833351 + stop: 1685951465.835259 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: ]> + pytest_pyfunc_call [hook] + pyfuncitem: ]> + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: ]' when='call' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script\n [-h] --foo.one FOO.ONE --foo.two FOO.TWO [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --foo.one FOO.ONE\n --foo.two FOO.TWO\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'")] + duration: 0.6442673579995244 + start: 1685951465.835901 + stop: 1685951466.480154 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: ]> + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: ]> + call: + finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: ]' when='teardown' outcome='passed'> + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + keywords: {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script\n [-h] --foo.one FOO.ONE --foo.two FOO.TWO [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --foo.one FOO.ONE\n --foo.two FOO.TWO\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'")] + duration: 0.00038592599958064966 + start: 1685951466.4809642 + stop: 1685951466.481351 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparser_with_doc + location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparser_with_doc + location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') + keywords: {'test_argparser_with_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0002025419998972211 + start: 1685951466.483218 + stop: 1685951466.4834208 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparser_with_doc + location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') + keywords: {'test_argparser_with_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'")] + duration: 0.011666497999613057 + start: 1685951466.483816 + stop: 1685951466.4954839 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparser_with_doc + location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') + keywords: {'test_argparser_with_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'")] + duration: 0.0002207099996667239 + start: 1685951466.496104 + stop: 1685951466.496326 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparser_with_doc + location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> ['--file_paths', '/home/bart/cwl_test/test2'] [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> ['/home/bart/cwl_test/test2'] [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]') + keywords: {'test_argparse_append_with_default[job_order1-expected_values1]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order1-expected_values1': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0005410029998529353 + start: 1685951466.498595 + stop: 1685951466.499137 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]') + keywords: {'test_argparse_append_with_default[job_order1-expected_values1]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order1-expected_values1': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")] + duration: 0.8447297829998206 + start: 1685951466.49974 + stop: 1685951467.3444512 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]') + keywords: {'test_argparse_append_with_default[job_order1-expected_values1]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order1-expected_values1': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")] + duration: 0.0003429710004638764 + start: 1685951467.345119 + stop: 1685951467.345463 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order2-expected_values2] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order2-expected_values2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> ['--file_paths', '/home/bart/cwl_test/test2', '--file_paths', '/home/bart/cwl_test/test3'] [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> ['/home/bart/cwl_test/test2', '/home/bart/cwl_test/test3'] [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order2-expected_values2] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order2-expected_values2]') + keywords: {'test_argparse_append_with_default[job_order2-expected_values2]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order2-expected_values2': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0004941550005241879 + start: 1685951467.347192 + stop: 1685951467.347687 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order2-expected_values2] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order2-expected_values2]') + keywords: {'test_argparse_append_with_default[job_order2-expected_values2]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order2-expected_values2': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")] + duration: 0.0167755689999467 + start: 1685951467.3482409 + stop: 1685951467.3650181 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order2-expected_values2] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order2-expected_values2]') + keywords: {'test_argparse_append_with_default[job_order2-expected_values2]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order2-expected_values2': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")] + duration: 0.0003022480004801764 + start: 1685951467.365503 + stop: 1685951467.365806 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order2-expected_values2] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order2-expected_values2]') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js + location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js + location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') + keywords: {'test_js_hint_reports_invalid_js': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00031787399984750664 + start: 1685951467.368246 + stop: 1685951467.368565 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js + location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') + keywords: {'test_js_hint_reports_invalid_js': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.013302664000548248 + start: 1685951467.369011 + stop: 1685951467.382315 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js + location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') + keywords: {'test_js_hint_reports_invalid_js': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0002095480003845296 + start: 1685951467.3827882 + stop: 1685951467.3830001 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js + location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_js_hint_warn_on_es6 + location: ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_warn_on_es6 + location: ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6') + keywords: {'test_js_hint_warn_on_es6': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0002407930005574599 + start: 1685951467.385212 + stop: 1685951467.3854542 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_warn_on_es6 + location: ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6') + keywords: {'test_js_hint_warn_on_es6': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.008448042999589234 + start: 1685951467.386027 + stop: 1685951467.394476 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_warn_on_es6 + location: ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6') + keywords: {'test_js_hint_warn_on_es6': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0002241669999420992 + start: 1685951467.395021 + stop: 1685951467.3952472 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_js_hint_warn_on_es6 + location: ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_js_hint_error_on_undefined_name + location: ('tests/test_validate_js.py', 74, 'test_js_hint_error_on_undefined_name') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_error_on_undefined_name + location: ('tests/test_validate_js.py', 74, 'test_js_hint_error_on_undefined_name') + keywords: {'test_js_hint_error_on_undefined_name': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00031343499995273305 + start: 1685951467.397362 + stop: 1685951467.397677 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_error_on_undefined_name + location: ('tests/test_validate_js.py', 74, 'test_js_hint_error_on_undefined_name') + keywords: {'test_js_hint_error_on_undefined_name': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.010393013000793871 + start: 1685951467.398325 + stop: 1685951467.4087198 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_error_on_undefined_name + location: ('tests/test_validate_js.py', 74, 'test_js_hint_error_on_undefined_name') + keywords: {'test_js_hint_error_on_undefined_name': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00035033899985137396 + start: 1685951467.4096682 + stop: 1685951467.41002 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_js_hint_error_on_undefined_name + location: ('tests/test_validate_js.py', 74, 'test_js_hint_error_on_undefined_name') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_js_hint_set_defined_name + location: ('tests/test_validate_js.py', 78, 'test_js_hint_set_defined_name') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_set_defined_name + location: ('tests/test_validate_js.py', 78, 'test_js_hint_set_defined_name') + keywords: {'test_js_hint_set_defined_name': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0003560980003385339 + start: 1685951467.4127629 + stop: 1685951467.413121 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_set_defined_name + location: ('tests/test_validate_js.py', 78, 'test_js_hint_set_defined_name') + keywords: {'test_js_hint_set_defined_name': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.006926598000063677 + start: 1685951467.413738 + stop: 1685951467.4206662 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_validate_js.py::test_js_hint_set_defined_name + location: ('tests/test_validate_js.py', 78, 'test_js_hint_set_defined_name') + keywords: {'test_js_hint_set_defined_name': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00020684699939010898 + start: 1685951467.421165 + stop: 1685951467.421373 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_js_hint_set_defined_name + location: ('tests/test_validate_js.py', 78, 'test_js_hint_set_defined_name') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: None + pytest_runtest_logstart [hook] + nodeid: tests/test_windows_warning.py::test_windows_warning + location: ('tests/test_windows_warning.py', 12, 'test_windows_warning') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x10c1a06d0> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_windows_warning.py::test_windows_warning + location: ('tests/test_windows_warning.py', 12, 'test_windows_warning') + keywords: {'test_windows_warning': 1, 'test_windows_warning.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0007037330005914555 + start: 1685951467.4243672 + stop: 1685951467.425073 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_windows_warning.py::test_windows_warning + location: ('tests/test_windows_warning.py', 12, 'test_windows_warning') + keywords: {'test_windows_warning': 1, 'test_windows_warning.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [] + duration: 0.0006785279992982396 + start: 1685951467.4255328 + stop: 1685951467.426213 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: None + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: ]>> + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x1092a7730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_windows_warning.py::test_windows_warning + location: ('tests/test_windows_warning.py', 12, 'test_windows_warning') + keywords: {'test_windows_warning': 1, 'test_windows_warning.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.004307549000259314 + start: 1685951467.426868 + stop: 1685951467.431178 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_windows_warning.py::test_windows_warning + location: ('tests/test_windows_warning.py', 12, 'test_windows_warning') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + finish pytest_runtestloop --> True [hook] + pytest_sessionfinish [hook] + session: testsfailed=2 testscollected=664> + exitstatus: 1 + finish pytest_sessionfinish --> [] [hook] + pytest_unconfigure [hook] + config: <_pytest.config.Config object at 0x1092a7730> + finish pytest_unconfigure --> [] [hook] +_research_object_picklability' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_research_object_picklability + location: ('tests/test_provenance.py', 788, 'test_research_object_picklability') + keywords: {'test_research_object_picklability': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj')] + duration: 0.00234540899964486 + start: 1685951451.797377 + stop: 1685951451.799724 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_research_object_picklability + location: ('tests/test_provenance.py', 788, 'test_research_object_picklability') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_directory_workflow_no_listing + location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_directory_workflow_no_listing + location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') + keywords: {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0016229729999395204 + start: 1685951451.801435 + stop: 1685951451.80306 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + early skip of rewriting module: encodings.ascii [assertion] + early skip of rewriting module: rdflib.plugins.parsers.jsonld [assertion] + early skip of rewriting module: rdflib.plugins.shared [assertion] + early skip of rewriting module: rdflib.plugins.shared.jsonld [assertion] + early skip of rewriting module: rdflib.plugins.shared.jsonld.context [assertion] + early skip of rewriting module: rdflib.plugins.shared.jsonld.errors [assertion] + early skip of rewriting module: rdflib.plugins.shared.jsonld.keys [assertion] + early skip of rewriting module: rdflib.plugins.shared.jsonld.util [assertion] + early skip of rewriting module: rdflib.plugins.serializers [assertion] + early skip of rewriting module: rdflib.plugins.serializers.turtle [assertion] + early skip of rewriting module: prov.serializers.provjson [assertion] + early skip of rewriting module: prov.serializers.provn [assertion] + early skip of rewriting module: prov.serializers.provxml [assertion] + early skip of rewriting module: prov.serializers.provrdf [assertion] + early skip of rewriting module: rdflib.plugins.serializers.nt [assertion] + early skip of rewriting module: rdflib.plugins.serializers.jsonld [assertion] + pytest_runtest_makereport [hook] + item: + call: > + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_directory_workflow_no_listing + location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') + keywords: {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: failed + longrepr: {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 891, 'message': "AssertionError: assert not True\n + where True = ()\n + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"}, 'reprtraceback': {'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_directory_workflow_no_listing(tmp_path: Path) -> None:', ' """', ' This test will check for 3 files that should be there and 3 files that should not be there.', ' @param tmp_path:', ' """', ' ', ' dir2 = tmp_path / "dir_deep_listing"', ' dir2.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in a b c ; do echo -n $x | sha1sum ; done', ' "a": "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",', ' "b": "e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",', ' "c": "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",', ' }', ' for x in "abc":', ' # Make test files with predictable hashes', ' with open(dir2 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir3 = tmp_path / "dir_no_listing"', ' dir3.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in d e f ; do echo -n $x | sha1sum ; done', ' "d": "3c363836cf4e16666669a25da280a1865c2d2874",', ' "e": "58e6b3a414a1e090dfc6029add0f3555ccba127f",', ' "f": "4a0a19218e082a343a1b17e5333409af9d98f0f5",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir3 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir4 = tmp_path / "dir_no_info"', ' dir4.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in g h i ; do echo -n $x | sha1sum ; done', ' "g": "54fd1711209fb1c0781092374132c66e79e2241b",', ' "h": "27d5482eebd075de44389774fce28c69f45c8a75",', ' "i": "042dc4512fa3d391c5170cf3aa61e6a638f84342",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir4 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/directory_no_listing.cwl"),', ' "--dir",', ' str(dir2),', ' "--ignore",', ' str(dir3),', ' "--ignore_no_info",', ' str(dir4),', ' )', ' ', ' # Visualize the path structure', ' list_files(tmp_path)', ' ', ' # check invert? as there should be no data in there', ' # check_provenance(folder, directory=True)', ' ', ' # Output should include ls stdout of filenames a b c on each line', ' file_list = (', ' folder', ' / "data"', ' / "84"', ' / "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4"', ' # checksum as returned from:', ' # echo -e "a\\nb\\nc" | sha1sum', ' # 3ca69e8d6c234a469d16ac28a4a658c92267c423 -', ' )', ' # File should not exist...', '> assert not file_list.is_file()', 'E AssertionError: assert not True', "E + where True = ()", "E + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 891, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, 'sections': [], 'chain': [({'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_directory_workflow_no_listing(tmp_path: Path) -> None:', ' """', ' This test will check for 3 files that should be there and 3 files that should not be there.', ' @param tmp_path:', ' """', ' ', ' dir2 = tmp_path / "dir_deep_listing"', ' dir2.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in a b c ; do echo -n $x | sha1sum ; done', ' "a": "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",', ' "b": "e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",', ' "c": "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",', ' }', ' for x in "abc":', ' # Make test files with predictable hashes', ' with open(dir2 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir3 = tmp_path / "dir_no_listing"', ' dir3.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in d e f ; do echo -n $x | sha1sum ; done', ' "d": "3c363836cf4e16666669a25da280a1865c2d2874",', ' "e": "58e6b3a414a1e090dfc6029add0f3555ccba127f",', ' "f": "4a0a19218e082a343a1b17e5333409af9d98f0f5",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir3 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir4 = tmp_path / "dir_no_info"', ' dir4.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in g h i ; do echo -n $x | sha1sum ; done', ' "g": "54fd1711209fb1c0781092374132c66e79e2241b",', ' "h": "27d5482eebd075de44389774fce28c69f45c8a75",', ' "i": "042dc4512fa3d391c5170cf3aa61e6a638f84342",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir4 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/directory_no_listing.cwl"),', ' "--dir",', ' str(dir2),', ' "--ignore",', ' str(dir3),', ' "--ignore_no_info",', ' str(dir4),', ' )', ' ', ' # Visualize the path structure', ' list_files(tmp_path)', ' ', ' # check invert? as there should be no data in there', ' # check_provenance(folder, directory=True)', ' ', ' # Output should include ls stdout of filenames a b c on each line', ' file_list = (', ' folder', ' / "data"', ' / "84"', ' / "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4"', ' # checksum as returned from:', ' # echo -e "a\\nb\\nc" | sha1sum', ' # 3ca69e8d6c234a469d16ac28a4a658c92267c423 -', ' )', ' # File should not exist...', '> assert not file_list.is_file()', 'E AssertionError: assert not True', "E + where True = ()", "E + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 891, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 891, 'message': "AssertionError: assert not True\n + where True = ()\n + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"}, None)]} + when: call + user_properties: [] + sections: [('Captured stdout call', '{\n "output_1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad"\n },\n "output_2": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0\ntest_directory_workflow_no_lis0/\n cwltool-run/\n 511f5ede99eeae60df68dedf0f5a3c2886774dad\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir_no_info/\n f\n d\n e\n dir_deep_listing/\n a\n c\n b\n dir_no_listing/\n f\n d\n e\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory_no_listing.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3c363836cf4e16666669a25da280a1865c2d2874\n 58/\n 58e6b3a414a1e090dfc6029add0f3555ccba127f\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n a0/\n a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n 4a/\n 4a0a19218e082a343a1b17e5333409af9d98f0f5\n metadata/\n directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n manifest.json\n directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n logs/\n engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/KKDWnh\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'--ignore\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'--ignore_no_info\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: bf9a8c91a428be6becd92c778c02c67d427411a8 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f63ffc058c8cfdb908506337c548afa6df073ae4c60dfd126529041314a548a5 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4fd8262b0744c271fe42c0c7a3142522708348559d0e405bb03bf2ab6becbeb7f64fecd3d8fb0762aa478fd99791200d9c3503e2e2e47b16546bd96fda2bca33 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing"\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}, \'ignore\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}, \'ignore_no_info\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_deep_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_info\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: b8ccdd89c80eca48567812797b860122d330b485 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: c1d4042283d1ce80021fa05c18eed2ae1bffea933f49ddd960b4a09f9a262cb5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: bdc150fa3761c3d002efb9be43f71cf8dac2e1f42259fdff201f185d0603839f2b882baf2cf28656ecfdfa1519fdf92a6b8611fab87b17604c45c09e28ed72ee workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ba113d80556b23c15fd7c2455789b16fe31f2335 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9ae22ea23ca80ffebd84f7e8ff4b640ec2d0f1956c56555485252b0f43892ce6 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 2b38d01f508e3abb2d8249e19be4d222e1b13c37943489f70523fa076f09d012a4f139a3b480706cd411ec961a4f8dcb5b255404f7f71fa74a24bf1886f66889 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 4a0a19218e082a343a1b17e5333409af9d98f0f5 data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 3c363836cf4e16666669a25da280a1865c2d2874 data/3c/3c363836cf4e16666669a25da280a1865c2d2874\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 58e6b3a414a1e090dfc6029add0f3555ccba127f data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 2de598f6b273e2eaaabca9703f0ca739ac4fb4bd metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 803eefe7af4871fc1029330cf00afb4abc33e44591400b6036c887ce4d3516c8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 26f9234c3e7852c13da1a41405bba99f80817d45abf0beed442c3c31cd106afb3b4bdc96fced5ce6e84194af3d156b1c880cef95d9283e3a98f6a87af04e40b8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 94788d2e8451e82a089085ce9a13d21d7648a56a metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: be9b32c701e852c1cce196ed17bb7d04ce147cda1847a2bb31b81a0b3b3bdfb8 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 7f08203a26bde01dd72f0888a87167b6ac571b24e88928de1d73b3cdfcd873e5576f2ccb107b88fa663be20691607e6c74c57f73e2ab5acfa2da3ab1242a5465 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info",\n "basename": "dir_no_info"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from _:c64797b9-0e72-438b-b250-9a183c2486c6 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a01f4d65bf45da813bc5c1482c403b467537faba metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b68aeee0d249094334ad30ea74bf2e8e13de8620ffba8d87dd4ff03f4f707c9 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 0508e90f315884b3b5652850fe11970d60be330ecc6079e443b6f9cf8cdd539ccd6f0f679d05b0ee5c9da1550a3ca81b79425c9b07bca981a24338d10441f318 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 456e3bd591c3db18d15eb03f1b0033f71af12d3a metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 0b6bb416adfdfd452957e1ece6c05a5065835bb85234d7946a264c4016248028 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 856999b9b5ec46248fac41601440d838ba31b12e7c942005522d5e3ef91ebc7edd707457acdfc7d46895a185beb5785592c34d596e22cfb805edc527fc62a209 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9c22bec2e40d921fa850aa5fff207217b2700033 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f8c81c1297aa21b9e5e6d72fbdd4d5bb4dbc5fcc7a8332e4eb07cc6af6620171 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 59200606c8f78dec7b9c4ee540aa62a420c89b773788766589cc20849df29bc5ad624c61cd642b3eb214ab9d94598f99d290690e5e9668690398e7fee40211c3 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmpuu8p9qg8\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmpgouh1jdv\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from _:6798550b-35c6-4878-b539-969960c2ddd6 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "Directory",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n }\n ],\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f"\n }\n },\n {\n "position": [\n 2,\n "ignore"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing",\n "path": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "dirname": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 8cc5feedb2b21504d21859e0f63631f0b517553b metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b0f753abd9f52fa7bda09156130e6b0b936f1cd0705a6894db0eadff26b12a1 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: d6d5e13b344294994185ebcff17d42825d055b22a1e88978298377197522f2542db43987450874f4fd8da234a974070ce23ac03eff61c0a5a647d4c97a68cec6 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 18386d0fde6d11e92ff3eb4475f6553b3093c775 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 31c7501fcee1311e24b50b4142dc0321239dbdaaf821e84c7370321898b234d3 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: be3cf5fc2ba70daafbc4cfe1fe3dd41ee9772f0cccd8f955aa6b0c619abb9eda2bc00818090ad245ffe663fb8151f5b965feb7f4933e3ce68e7d38ff89aa3587 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: a0ce0441f957dcde10291470aa5062ffc7cbdf8c data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "output_1": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n },\n "output_2": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmphgdo2k_m\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmpy12k7j25\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp30294ykg/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe4wl6xjm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp30294ykg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp03q_qnzm\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 831d591ea563d82200f6b29cdbed89958af99946 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8591aab1f32872e19f186118be1462101272c003e5725780ad0a1053b4f45b8 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 1b73e532287cafb4438cfc69dd62ca998d374d25d2d2a9e1aae2d80da74193ec8abc5494227ed037b4a9cbcebd72b4ba2f5c5a995fc9406ad87abc08a421237a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 52917a96deb1331e4f3e0d0c0ca5c06da11b550f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 952621e5f975fa4b8536d1246e03019673efe29716be7dd946885b26420ad858 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 9d13a8b2e9919c7d90a5b65c0af7326c4869efebe2b1525d1dee1d573159349fa8c3d9a06386e6e3054b4517ac86f5389bb90d9cc8105857baa9a142a9958123 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 4660384a529ef8217263414cfe7d8e09a36dae6a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8d43e02f50436e6bc3d92fdf3f37d0452a90fb55cc177c4902b62802ce733b8 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: c3a8205627d56adebcf5e2221b0ce6adc18bebc2af049dbec6dd744c90d1d704cca928860c5b41a8c0fa7056484ca8a454555ab058b982a5a5b3c4b48e35de1d metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: de4b6608f9e3af201c70ff6b53f85749a8492405 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: fadae5349308a66d763eacbe40b6c0348bdfd6947a138a8f8adab6c451836db5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4eb4037e059930960700522093a233245189d1e1284b785d7642142d07ace00ecb89da2a98af756469be68dec3c3b6b0e41368ad4b0325b536fffb642fdc0280 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 153127a4ee5a028d1acd636b0809d434d53da02d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 717a4f8ae33902dcd217991e923892a59b626fe60f616d3cd275806d18e9da4a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 5c8ece230a9c9d65f0b953c27045f92d27e3d6ecc3823e7ef9d3cb4426d66ded6a1fddd45a4bfed846940ed9a1f4bc3f4e9159650a856e9c7bdde1a7162f4ead metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9a047fa31e52f7b66c1a7cebf88c57d9e388c8c6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: a727a73f4d563af8f90316d9ec809d0f853abc53632d2f306ca2944475293cdc metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 83f351fed5f621fa4763e6d0f0762964aa213f325926bf7c406e94eef34970695b9c599bfbd807565b497858edbdfbacc1c3001cbdfb54bb826e49da09ee004f metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'output_1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}, \'output_2\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': 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\'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a259a2ddea0fb8dbe04ce95431c7b87d74444c8d workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f92dbdf72304f179e312894c469c59f4b08ddabf26264f1ad7a38aa6a527b39e workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 586e6634367c1f8cddf3f26d6e2c7ff826ce3677902c23890028d73f66b854b30eb013b70cecaefb3fdcb8f47fe266e7182f62f24b6f5d94973d73b7dbc04479 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 757937dc88f5d446a6e63c9d1f12acde32b02ecd snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 2c725914f45b19c49b5a6e9540477b70a0273cefdbd82c19de19054de16cb24f snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6d058c8a26fad02c7935f0ee249b186701f49d64ed43f8dccc87ca2f374356b971470006906e36f6d9c888cf50ead1e3fe3f6759e8d1d53a678ca6c1a171387a snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ec85041b357ff2b39338cfbc69d2560640966f89 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 36a504d2c4551667e228d84c4eed90bd73747fe98606b30d912ec9b1ec3767bd metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: f2e20d11de50af96dc8e3bfcd43f0bc8d78342dda00c88c80de92a8f04d4aa3bbf684bf7c59f342cb8ef84393e00327a65b1c107d18f4a449e6116496d5e1f54 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0033518ae68cb74ef1d56196451d0ac9957ce80f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 640cf34ac826eeba52a190d69e5d9f3e0cd8025e6c6a20a5c32c5a479c687c67 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6345ca41b6e0eedc5d3dc2a171ce96cb26aef6a6072f27634478eee2492ac756794ece6fd4949d827a922b55d0d2d7fd5c66b69ade15549c3b96aef4b86e9d0a metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0d2331dab4d408bceb1057cfe5f1e826e1990c29 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 37908e47bb9f9ca212410631fd36ca1f333b9640b281b15639bfc1a822730ba6 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 059ed78b311c6402fb86010caf6283f0bd799fc922264bbef8b82bfb774e14680d16ee89810d4a50f82511d03a2a7596afe8806d3137f4c749d9db1e3b533ca2 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance')] + duration: 4.963674428999184 + start: 1685951451.80366 + stop: 1685951456.767212 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_exception_interact [hook] + node: + call: > + report: + finish pytest_exception_interact --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_provenance.py::test_directory_workflow_no_listing + location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') + keywords: {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '{\n "output_1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad"\n },\n "output_2": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0\ntest_directory_workflow_no_lis0/\n cwltool-run/\n 511f5ede99eeae60df68dedf0f5a3c2886774dad\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir_no_info/\n f\n d\n e\n dir_deep_listing/\n a\n c\n b\n dir_no_listing/\n f\n d\n e\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory_no_listing.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3c363836cf4e16666669a25da280a1865c2d2874\n 58/\n 58e6b3a414a1e090dfc6029add0f3555ccba127f\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n a0/\n a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n 4a/\n 4a0a19218e082a343a1b17e5333409af9d98f0f5\n metadata/\n directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n manifest.json\n directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n logs/\n engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/KKDWnh\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'--ignore\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'--ignore_no_info\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: bf9a8c91a428be6becd92c778c02c67d427411a8 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f63ffc058c8cfdb908506337c548afa6df073ae4c60dfd126529041314a548a5 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4fd8262b0744c271fe42c0c7a3142522708348559d0e405bb03bf2ab6becbeb7f64fecd3d8fb0762aa478fd99791200d9c3503e2e2e47b16546bd96fda2bca33 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing"\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}, \'ignore\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}, \'ignore_no_info\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_deep_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_info\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: b8ccdd89c80eca48567812797b860122d330b485 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: c1d4042283d1ce80021fa05c18eed2ae1bffea933f49ddd960b4a09f9a262cb5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: bdc150fa3761c3d002efb9be43f71cf8dac2e1f42259fdff201f185d0603839f2b882baf2cf28656ecfdfa1519fdf92a6b8611fab87b17604c45c09e28ed72ee workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ba113d80556b23c15fd7c2455789b16fe31f2335 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9ae22ea23ca80ffebd84f7e8ff4b640ec2d0f1956c56555485252b0f43892ce6 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 2b38d01f508e3abb2d8249e19be4d222e1b13c37943489f70523fa076f09d012a4f139a3b480706cd411ec961a4f8dcb5b255404f7f71fa74a24bf1886f66889 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 4a0a19218e082a343a1b17e5333409af9d98f0f5 data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 3c363836cf4e16666669a25da280a1865c2d2874 data/3c/3c363836cf4e16666669a25da280a1865c2d2874\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 58e6b3a414a1e090dfc6029add0f3555ccba127f data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 2de598f6b273e2eaaabca9703f0ca739ac4fb4bd metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 803eefe7af4871fc1029330cf00afb4abc33e44591400b6036c887ce4d3516c8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 26f9234c3e7852c13da1a41405bba99f80817d45abf0beed442c3c31cd106afb3b4bdc96fced5ce6e84194af3d156b1c880cef95d9283e3a98f6a87af04e40b8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 94788d2e8451e82a089085ce9a13d21d7648a56a metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: be9b32c701e852c1cce196ed17bb7d04ce147cda1847a2bb31b81a0b3b3bdfb8 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 7f08203a26bde01dd72f0888a87167b6ac571b24e88928de1d73b3cdfcd873e5576f2ccb107b88fa663be20691607e6c74c57f73e2ab5acfa2da3ab1242a5465 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info",\n "basename": "dir_no_info"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from _:c64797b9-0e72-438b-b250-9a183c2486c6 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a01f4d65bf45da813bc5c1482c403b467537faba metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b68aeee0d249094334ad30ea74bf2e8e13de8620ffba8d87dd4ff03f4f707c9 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 0508e90f315884b3b5652850fe11970d60be330ecc6079e443b6f9cf8cdd539ccd6f0f679d05b0ee5c9da1550a3ca81b79425c9b07bca981a24338d10441f318 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 456e3bd591c3db18d15eb03f1b0033f71af12d3a metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 0b6bb416adfdfd452957e1ece6c05a5065835bb85234d7946a264c4016248028 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 856999b9b5ec46248fac41601440d838ba31b12e7c942005522d5e3ef91ebc7edd707457acdfc7d46895a185beb5785592c34d596e22cfb805edc527fc62a209 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9c22bec2e40d921fa850aa5fff207217b2700033 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f8c81c1297aa21b9e5e6d72fbdd4d5bb4dbc5fcc7a8332e4eb07cc6af6620171 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 59200606c8f78dec7b9c4ee540aa62a420c89b773788766589cc20849df29bc5ad624c61cd642b3eb214ab9d94598f99d290690e5e9668690398e7fee40211c3 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmpuu8p9qg8\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmpgouh1jdv\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from _:6798550b-35c6-4878-b539-969960c2ddd6 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "Directory",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n }\n ],\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f"\n }\n },\n {\n "position": [\n 2,\n "ignore"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing",\n "path": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "dirname": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 8cc5feedb2b21504d21859e0f63631f0b517553b metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b0f753abd9f52fa7bda09156130e6b0b936f1cd0705a6894db0eadff26b12a1 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: d6d5e13b344294994185ebcff17d42825d055b22a1e88978298377197522f2542db43987450874f4fd8da234a974070ce23ac03eff61c0a5a647d4c97a68cec6 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 18386d0fde6d11e92ff3eb4475f6553b3093c775 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 31c7501fcee1311e24b50b4142dc0321239dbdaaf821e84c7370321898b234d3 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: be3cf5fc2ba70daafbc4cfe1fe3dd41ee9772f0cccd8f955aa6b0c619abb9eda2bc00818090ad245ffe663fb8151f5b965feb7f4933e3ce68e7d38ff89aa3587 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: a0ce0441f957dcde10291470aa5062ffc7cbdf8c data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "output_1": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n },\n "output_2": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmphgdo2k_m\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmpy12k7j25\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp30294ykg/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe4wl6xjm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp30294ykg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp03q_qnzm\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 831d591ea563d82200f6b29cdbed89958af99946 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8591aab1f32872e19f186118be1462101272c003e5725780ad0a1053b4f45b8 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 1b73e532287cafb4438cfc69dd62ca998d374d25d2d2a9e1aae2d80da74193ec8abc5494227ed037b4a9cbcebd72b4ba2f5c5a995fc9406ad87abc08a421237a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 52917a96deb1331e4f3e0d0c0ca5c06da11b550f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 952621e5f975fa4b8536d1246e03019673efe29716be7dd946885b26420ad858 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 9d13a8b2e9919c7d90a5b65c0af7326c4869efebe2b1525d1dee1d573159349fa8c3d9a06386e6e3054b4517ac86f5389bb90d9cc8105857baa9a142a9958123 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 4660384a529ef8217263414cfe7d8e09a36dae6a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8d43e02f50436e6bc3d92fdf3f37d0452a90fb55cc177c4902b62802ce733b8 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: c3a8205627d56adebcf5e2221b0ce6adc18bebc2af049dbec6dd744c90d1d704cca928860c5b41a8c0fa7056484ca8a454555ab058b982a5a5b3c4b48e35de1d metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: de4b6608f9e3af201c70ff6b53f85749a8492405 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: fadae5349308a66d763eacbe40b6c0348bdfd6947a138a8f8adab6c451836db5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4eb4037e059930960700522093a233245189d1e1284b785d7642142d07ace00ecb89da2a98af756469be68dec3c3b6b0e41368ad4b0325b536fffb642fdc0280 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 153127a4ee5a028d1acd636b0809d434d53da02d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 717a4f8ae33902dcd217991e923892a59b626fe60f616d3cd275806d18e9da4a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 5c8ece230a9c9d65f0b953c27045f92d27e3d6ecc3823e7ef9d3cb4426d66ded6a1fddd45a4bfed846940ed9a1f4bc3f4e9159650a856e9c7bdde1a7162f4ead metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9a047fa31e52f7b66c1a7cebf88c57d9e388c8c6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: a727a73f4d563af8f90316d9ec809d0f853abc53632d2f306ca2944475293cdc metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 83f351fed5f621fa4763e6d0f0762964aa213f325926bf7c406e94eef34970695b9c599bfbd807565b497858edbdfbacc1c3001cbdfb54bb826e49da09ee004f metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'output_1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}, \'output_2\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 153\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a259a2ddea0fb8dbe04ce95431c7b87d74444c8d workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f92dbdf72304f179e312894c469c59f4b08ddabf26264f1ad7a38aa6a527b39e workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 586e6634367c1f8cddf3f26d6e2c7ff826ce3677902c23890028d73f66b854b30eb013b70cecaefb3fdcb8f47fe266e7182f62f24b6f5d94973d73b7dbc04479 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 757937dc88f5d446a6e63c9d1f12acde32b02ecd snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 2c725914f45b19c49b5a6e9540477b70a0273cefdbd82c19de19054de16cb24f snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6d058c8a26fad02c7935f0ee249b186701f49d64ed43f8dccc87ca2f374356b971470006906e36f6d9c888cf50ead1e3fe3f6759e8d1d53a678ca6c1a171387a snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ec85041b357ff2b39338cfbc69d2560640966f89 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 36a504d2c4551667e228d84c4eed90bd73747fe98606b30d912ec9b1ec3767bd metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: f2e20d11de50af96dc8e3bfcd43f0bc8d78342dda00c88c80de92a8f04d4aa3bbf684bf7c59f342cb8ef84393e00327a65b1c107d18f4a449e6116496d5e1f54 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0033518ae68cb74ef1d56196451d0ac9957ce80f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 640cf34ac826eeba52a190d69e5d9f3e0cd8025e6c6a20a5c32c5a479c687c67 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6345ca41b6e0eedc5d3dc2a171ce96cb26aef6a6072f27634478eee2492ac756794ece6fd4949d827a922b55d0d2d7fd5c66b69ade15549c3b96aef4b86e9d0a metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0d2331dab4d408bceb1057cfe5f1e826e1990c29 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 37908e47bb9f9ca212410631fd36ca1f333b9640b281b15639bfc1a822730ba6 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 059ed78b311c6402fb86010caf6283f0bd799fc922264bbef8b82bfb774e14680d16ee89810d4a50f82511d03a2a7596afe8806d3137f4c749d9db1e3b533ca2 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance')] + duration: 0.00152142999922944 + start: 1685951456.977313 + stop: 1685951456.978837 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_directory_workflow_no_listing + location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + nodeid: tests/test_provenance.py::test_directory_workflow_no_listing + when: runtest + location: None + finish pytest_warning_recorded --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print + location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print + location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') + keywords: {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0003581160008252482 + start: 1685951456.985954 + stop: 1685951456.986314 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print + location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') + keywords: {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '@prefix CommandLineBinding: .\n@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n cwl:inputBinding [ CommandLineBinding:position 1 ] ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'")] + duration: 0.6995283690002907 + start: 1685951456.986822 + stop: 1685951457.686334 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print + location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') + keywords: {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '@prefix CommandLineBinding: .\n@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n cwl:inputBinding [ CommandLineBinding:position 1 ] ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'")] + duration: 0.00019048600006499328 + start: 1685951457.686794 + stop: 1685951457.686985 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print + location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print_unicode + location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x10db8d870> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print_unicode + location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') + keywords: {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0005043370001658332 + start: 1685951457.688944 + stop: 1685951457.68945 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print_unicode + location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') + keywords: {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stdout call', '@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix rdfs: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n rdfs:label "Sequence file in FASTA format" ;\n rdfs:comment """Input sequence file in FASTA format (not compressed/zipped!).\nCan be an assembled genome (genome mode) or transcriptome (DNA,\ntranscriptome mode), or protein sequences from an annotated gene set\n(proteins mode).\nNB: select just one transcript/protein per gene for your input,\notherwise they will appear as ‘Duplicated’ matches.\n""" ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m /Users/jasperk/gitlab/cwltool/cwltool/__main__.py 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl'\n")] + duration: 1.9449515790001897 + start: 1685951457.6899168 + stop: 1685951459.634825 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print_unicode + location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') + keywords: {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stdout call', '@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix rdfs: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n rdfs:label "Sequence file in FASTA format" ;\n rdfs:comment """Input sequence file in FASTA format (not compressed/zipped!).\nCan be an assembled genome (genome mode) or transcriptome (DNA,\ntranscriptome mode), or protein sequences from an annotated gene set\n(proteins mode).\nNB: select just one transcript/protein per gene for your input,\notherwise they will appear as ‘Duplicated’ matches.\n""" ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m /Users/jasperk/gitlab/cwltool/cwltool/__main__.py 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl'\n")] + duration: 0.0006568690005224198 + start: 1685951459.6365361 + stop: 1685951459.637194 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print_unicode + location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity.py::test_singularity_iwdr + location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_singularity_iwdr0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_singularity_iwdr0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x10db8d3f0> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_singularity.py::test_singularity_iwdr + location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') + keywords: {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.002171388000533625 + start: 1685951459.638792 + stop: 1685951459.6409652 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_singularity.py::test_singularity_iwdr + location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') + keywords: {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:810 Singularity error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 771, in run\n self.get_from_requirements(\n File "/Users/jasperk/gitlab/cwltool/cwltool/singularity.py", line 292, in get_from_requirements\n raise WorkflowException("singularity executable is not available")\ncwltool.errors.WorkflowException: singularity executable is not available\nERROR cwltool:main.py:1373 Workflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available')] + duration: 0.7381495270001324 + start: 1685951459.641752 + stop: 1685951460.379884 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_singularity.py::test_singularity_iwdr + location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') + keywords: {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:810 Singularity error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 771, in run\n self.get_from_requirements(\n File "/Users/jasperk/gitlab/cwltool/cwltool/singularity.py", line 292, in get_from_requirements\n raise WorkflowException("singularity executable is not available")\ncwltool.errors.WorkflowException: singularity executable is not available\nERROR cwltool:main.py:1373 Workflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available')] + duration: 0.00043232999996689614 + start: 1685951460.380364 + stop: 1685951460.3807979 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_singularity.py::test_singularity_iwdr + location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull + location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_runtest_makereport [hook] + item: + call: > + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull + location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') + keywords: {'test_singularity_incorrect_image_pull': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: skipped + longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 84, 'Skipped: Requires the singularity executable on the system path.') + when: setup + user_properties: [] + sections: [] + duration: 0.00022189900028024567 + start: 1685951460.381962 + stop: 1685951460.382185 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull + location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') + keywords: {'test_singularity_incorrect_image_pull': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.00021053000000392785 + start: 1685951460.382848 + stop: 1685951460.38306 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull + location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity.py::test_singularity_local + location: ('tests/test_singularity.py', 98, 'test_singularity_local') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_runtest_makereport [hook] + item: + call: > + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_singularity.py::test_singularity_local + location: ('tests/test_singularity.py', 98, 'test_singularity_local') + keywords: {'test_singularity_local': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: skipped + longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 99, 'Skipped: Requires the singularity executable on the system path.') + when: setup + user_properties: [] + sections: [] + duration: 0.0002089989993692143 + start: 1685951460.385066 + stop: 1685951460.3852758 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_singularity.py::test_singularity_local + location: ('tests/test_singularity.py', 98, 'test_singularity_local') + keywords: {'test_singularity_local': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [] + duration: 0.0002950230000351439 + start: 1685951460.38608 + stop: 1685951460.3863769 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_singularity.py::test_singularity_local + location: ('tests/test_singularity.py', 98, 'test_singularity_local') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step + location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step + location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') + keywords: {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.001556540999445133 + start: 1685951460.3884459 + stop: 1685951460.390004 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step + location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') + keywords: {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp65j863ig$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp65j863ig/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp65j863ig/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmp11jtljvb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpwn42k8_w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp65j863ig/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp65j863ig\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 1.1143909949996669 + start: 1685951460.390568 + stop: 1685951461.5049338 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step + location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') + keywords: {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp65j863ig$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp65j863ig/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp65j863ig/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmp11jtljvb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpwn42k8_w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp65j863ig/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp65j863ig\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0006726860001435853 + start: 1685951461.506804 + stop: 1685951461.507478 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step + location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step + location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0 [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step + location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') + keywords: {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.0021509959997274564 + start: 1685951461.510327 + stop: 1685951461.512479 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step + location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') + keywords: {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\'\nDEBUG cwltool:command_line_tool.py:982 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json#count-lines17-wf/step1/run/count-lines17-wf.cwl@step_step1@run/stepX/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run/stepY/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run\nDEBUG cwltool:command_line_tool.py:988 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initial work dir {}\nINFO cwltool:job.py:266 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] /private/tmp/docker_tmp_9yt0z8_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_9yt0z8_,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmprz9dykzk,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpsbmfwops/20230605095102-600646.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt > /private/tmp/docker_tmp_9yt0z8_/output\nINFO cwltool:job.py:905 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] completed success\nDEBUG cwltool:job.py:422 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_9yt0z8_/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing input staging directory /private/tmp/docker_tmp89udep8a\nDEBUG cwltool:job.py:454 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing temporary directory /private/tmp/docker_tmprz9dykzk\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_9yt0z8_/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_9yt0z8_\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 2.11600468800043 + start: 1685951461.5130591 + stop: 1685951463.6290119 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step + location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') + keywords: {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\'\nDEBUG cwltool:command_line_tool.py:982 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json#count-lines17-wf/step1/run/count-lines17-wf.cwl@step_step1@run/stepX/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run/stepY/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run\nDEBUG cwltool:command_line_tool.py:988 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initial work dir {}\nINFO cwltool:job.py:266 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] /private/tmp/docker_tmp_9yt0z8_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_9yt0z8_,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmprz9dykzk,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpsbmfwops/20230605095102-600646.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt > /private/tmp/docker_tmp_9yt0z8_/output\nINFO cwltool:job.py:905 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] completed success\nDEBUG cwltool:job.py:422 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_9yt0z8_/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing input staging directory /private/tmp/docker_tmp89udep8a\nDEBUG cwltool:job.py:454 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing temporary directory /private/tmp/docker_tmprz9dykzk\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_9yt0z8_/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_9yt0z8_\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.0008782109998719534 + start: 1685951463.630854 + stop: 1685951463.6317341 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step + location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value + location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value + location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') + keywords: {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.00043156799983989913 + start: 1685951463.634976 + stop: 1685951463.6354098 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value + location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') + keywords: {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', 'latest: Pulling from library/alpine\nDigest: sha256:02bb6f428431fbc2809c5d1b41eab5a68350194fb508869a33cb1af4444c9b11\nStatus: Image is up to date for alpine:latest\ndocker.io/library/alpine:latest\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:argparser.py:943 Can\'t make command line argument from Any\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "message": "two"\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step task2\nDEBUG cwltool:workflow_job.py:727 [step task2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2] start\nDEBUG cwltool:command_line_tool.py:982 [job task2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2\nDEBUG cwltool:command_line_tool.py:988 [job task2] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/alpine:latest\']\nDEBUG cwltool:job.py:215 [job task2] initial work dir {}\nINFO cwltool:job.py:266 [job task2] /private/tmp/docker_tmp2vpjz9j3$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2vpjz9j3,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpbyyklcxx,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpwtgdio32/20230605095106-754192.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2] completed success\nDEBUG cwltool:job.py:422 [job task2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2vpjz9j3/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {}\nDEBUG cwltool:job.py:446 [job task2] Removing input staging directory /private/tmp/docker_tmpy2a25zaq\nDEBUG cwltool:job.py:454 [job task2] Removing temporary directory /private/tmp/docker_tmpbyyklcxx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2vpjz9j3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpysive81g\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 4.140258484999322 + start: 1685951463.636079 + stop: 1685951467.776237 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value + location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') + keywords: {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', 'latest: Pulling from library/alpine\nDigest: sha256:02bb6f428431fbc2809c5d1b41eab5a68350194fb508869a33cb1af4444c9b11\nStatus: Image is up to date for alpine:latest\ndocker.io/library/alpine:latest\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:argparser.py:943 Can\'t make command line argument from Any\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "message": "two"\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step task2\nDEBUG cwltool:workflow_job.py:727 [step task2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2] start\nDEBUG cwltool:command_line_tool.py:982 [job task2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2\nDEBUG cwltool:command_line_tool.py:988 [job task2] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/alpine:latest\']\nDEBUG cwltool:job.py:215 [job task2] initial work dir {}\nINFO cwltool:job.py:266 [job task2] /private/tmp/docker_tmp2vpjz9j3$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2vpjz9j3,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpbyyklcxx,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpwtgdio32/20230605095106-754192.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2] completed success\nDEBUG cwltool:job.py:422 [job task2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2vpjz9j3/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {}\nDEBUG cwltool:job.py:446 [job task2] Removing input staging directory /private/tmp/docker_tmpy2a25zaq\nDEBUG cwltool:job.py:454 [job task2] Removing temporary directory /private/tmp/docker_tmpbyyklcxx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2vpjz9j3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpysive81g\nINFO cwltool:main.py:1366 Final process status is success')] + duration: 0.00046557099994970486 + start: 1685951467.777664 + stop: 1685951467.778131 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value + location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + pytest_runtest_protocol [hook] + item: + nextitem: None + pytest_runtest_logstart [hook] + nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix + location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_setup [hook] + item: + pytest_fixture_setup [hook] + fixturedef: + request: > + mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0 [config:tmpdir] + finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0 [hook] + pytest_fixture_setup [hook] + fixturedef: + request: > + finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x10d56f1c0> [hook] + finish pytest_runtest_setup --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix + location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') + keywords: {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: setup + user_properties: [] + sections: [] + duration: 0.002130539000063436 + start: 1685951467.780889 + stop: 1685951467.783021 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_call [hook] + item: + pytest_pyfunc_call [hook] + pyfuncitem: + finish pytest_pyfunc_call --> True [hook] + finish pytest_runtest_call --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix + location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') + keywords: {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: call + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']\n"), ('Captured log call', "INFO cwltool:docker.py:164 ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']")] + duration: 0.09524703099941689 + start: 1685951467.7836092 + stop: 1685951467.878856 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_teardown [hook] + item: + nextitem: None + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + pytest_fixture_post_finalizer [hook] + fixturedef: + request: > + finish pytest_fixture_post_finalizer --> [] [hook] + finish pytest_runtest_teardown --> [] [hook] + pytest_runtest_makereport [hook] + item: + call: + finish pytest_runtest_makereport --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_report_teststatus --> ('', '', '') [hook] + pytest_report_to_serializable [hook] + config: <_pytest.config.Config object at 0x10a90b730> + report: + finish pytest_report_to_serializable --> [hook] + nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix + location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') + keywords: {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} + outcome: passed + longrepr: None + when: teardown + user_properties: [] + sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']\n"), ('Captured log call', "INFO cwltool:docker.py:164 ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']")] + duration: 0.003588997999941057 + start: 1685951467.880084 + stop: 1685951467.8836741 + $report_type: TestReport + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix + location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') + finish pytest_runtest_logfinish --> [] [hook] + finish pytest_runtest_protocol --> True [hook] + finish pytest_runtestloop --> True [hook] + pytest_sessionfinish [hook] + session: testsfailed=1 testscollected=664> + exitstatus: 1 + finish pytest_sessionfinish --> [] [hook] + pytest_unconfigure [hook] + config: <_pytest.config.Config object at 0x10a90b730> + finish pytest_unconfigure --> [] [hook] +f80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_listing_v1_0', 'location': ('tests/test_ext.py', 63, 'test_listing_v1_0'), 'keywords': {'test_listing_v1_0': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl'\n\x1b[1;30mINFO\x1b[0m [job listing_v1_0.cwl] /private/tmp/docker_tmp48ro06s9$ echo \\\n /private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\n/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\n\x1b[1;30mINFO\x1b[0m [job listing_v1_0.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job listing_v1_0.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\nDEBUG cwltool:command_line_tool.py:988 [job listing_v1_0.cwl] {\n "d": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1",\n "basename": "tmp1",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2",\n "basename": "tmp2",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3",\n "basename": "tmp3",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep",\n "basename": ".gitkeep",\n "size": 0\n }\n ]\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job listing_v1_0.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3/.gitkeep",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job listing_v1_0.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.d.listing[0].listing[0])"\n }\n]\nDEBUG cwltool:job.py:215 [job listing_v1_0.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job listing_v1_0.cwl] /private/tmp/docker_tmp48ro06s9$ echo \\\n /private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job listing_v1_0.cwl] completed success\nDEBUG cwltool:job.py:422 [job listing_v1_0.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job listing_v1_0.cwl] Removing input staging directory /private/tmp/docker_tmp5au7853y\nDEBUG cwltool:job.py:454 [job listing_v1_0.cwl] Removing temporary directory /private/tmp/docker_tmps8sr21xg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp48ro06s9\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7399552670003686, 'start': 1685951432.334913, 'stop': 1685951433.074852, '$report_type': 'TestReport', 'item_index': 367, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_listing_v1_0', 'location': ('tests/test_ext.py', 63, 'test_listing_v1_0'), 'keywords': {'test_listing_v1_0': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl'\n\x1b[1;30mINFO\x1b[0m [job listing_v1_0.cwl] /private/tmp/docker_tmp48ro06s9$ echo \\\n /private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\n/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\n\x1b[1;30mINFO\x1b[0m [job listing_v1_0.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job listing_v1_0.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\nDEBUG cwltool:command_line_tool.py:988 [job listing_v1_0.cwl] {\n "d": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1",\n "basename": "tmp1",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2",\n "basename": "tmp2",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3",\n "basename": "tmp3",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep",\n "basename": ".gitkeep",\n "size": 0\n }\n ]\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job listing_v1_0.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3/.gitkeep",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job listing_v1_0.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.d.listing[0].listing[0])"\n }\n]\nDEBUG cwltool:job.py:215 [job listing_v1_0.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job listing_v1_0.cwl] /private/tmp/docker_tmp48ro06s9$ echo \\\n /private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job listing_v1_0.cwl] completed success\nDEBUG cwltool:job.py:422 [job listing_v1_0.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job listing_v1_0.cwl] Removing input staging directory /private/tmp/docker_tmp5au7853y\nDEBUG cwltool:job.py:454 [job listing_v1_0.cwl] Removing temporary directory /private/tmp/docker_tmps8sr21xg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp48ro06s9\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006402729995897971, 'start': 1685951433.076601, 'stop': 1685951433.0772438, '$report_type': 'TestReport', 'item_index': 367, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_listing_v1_0 + location: ('tests/test_ext.py', 63, 'test_listing_v1_0') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_ext.py::test_listing_v1_1 + location: ('tests/test_ext.py', 69, 'test_listing_v1_1') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_listing_v1_1', 'location': ('tests/test_ext.py', 69, 'test_listing_v1_1'), 'keywords': {'test_listing_v1_1': 1, 'skipif': 1, 'skip': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_ext.py', 70, 'Skipped: This is not the default behaviour yet'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002449390003675944, 'start': 1685951433.07875, 'stop': 1685951433.078996, '$report_type': 'TestReport', 'item_index': 368, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_listing_v1_1', 'location': ('tests/test_ext.py', 69, 'test_listing_v1_1'), 'keywords': {'test_listing_v1_1': 1, 'skipif': 1, 'skip': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00018128899955627276, 'start': 1685951433.079686, 'stop': 1685951433.079869, '$report_type': 'TestReport', 'item_index': 368, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_listing_v1_1 + location: ('tests/test_ext.py', 69, 'test_listing_v1_1') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_ext.py::test_double_overwrite + location: ('tests/test_ext.py', 76, 'test_double_overwrite') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_double_overwrite', 'location': ('tests/test_ext.py', 76, 'test_double_overwrite'), 'keywords': {'test_double_overwrite': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016091850002339925, 'start': 1685951433.08082, 'stop': 1685951433.08243, '$report_type': 'TestReport', 'item_index': 369, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_checklink_outputSource', 'location': ('tests/test_load_tool.py', 52, 'test_checklink_outputSource'), 'keywords': {'test_checklink_outputSource': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "[worker-gw3] received command runtests {'indices': [432, 433, 434, 435, 436, 437, 438, 439]}\n\x1b[32m[2023-06-05 09:50:32]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\n\x1b[32m[2023-06-05 09:50:33]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'")], 'duration': 0.2310436990001108, 'start': 1685951432.901361, 'stop': 1685951433.132401, '$report_type': 'TestReport', 'item_index': 412, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_checklink_outputSource', 'location': ('tests/test_load_tool.py', 52, 'test_checklink_outputSource'), 'keywords': {'test_checklink_outputSource': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "[worker-gw3] received command runtests {'indices': [432, 433, 434, 435, 436, 437, 438, 439]}\n\x1b[32m[2023-06-05 09:50:32]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\n\x1b[32m[2023-06-05 09:50:33]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'")], 'duration': 0.0003706219995365245, 'start': 1685951433.133274, 'stop': 1685951433.1336472, '$report_type': 'TestReport', 'item_index': 412, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_load_tool.py::test_checklink_outputSource + location: ('tests/test_load_tool.py', 52, 'test_checklink_outputSource') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_load_tool.py::test_load_graph_fragment + location: ('tests/test_load_tool.py', 65, 'test_load_graph_fragment') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment', 'location': ('tests/test_load_tool.py', 65, 'test_load_graph_fragment'), 'keywords': {'test_load_graph_fragment': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003440290001890389, 'start': 1685951433.135226, 'stop': 1685951433.135571, '$report_type': 'TestReport', 'item_index': 413, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment', 'location': ('tests/test_load_tool.py', 65, 'test_load_graph_fragment'), 'keywords': {'test_load_graph_fragment': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.1476936069993826, 'start': 1685951433.1362, 'stop': 1685951433.283893, '$report_type': 'TestReport', 'item_index': 413, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment', 'location': ('tests/test_load_tool.py', 65, 'test_load_graph_fragment'), 'keywords': {'test_load_graph_fragment': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002599459994598874, 'start': 1685951433.284791, 'stop': 1685951433.285053, '$report_type': 'TestReport', 'item_index': 413, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_load_tool.py::test_load_graph_fragment + location: ('tests/test_load_tool.py', 65, 'test_load_graph_fragment') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment_from_packed', 'location': ('tests/test_load_tool.py', 83, 'test_load_graph_fragment_from_packed'), 'keywords': {'test_load_graph_fragment_from_packed': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00026335099937568884, 'start': 1685951433.286043, 'stop': 1685951433.286308, '$report_type': 'TestReport', 'item_index': 414, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_load_tool.py::test_load_graph_fragment_from_packed + location: ('tests/test_load_tool.py', 83, 'test_load_graph_fragment_from_packed') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations', 'location': ('tests/test_iwdr.py', 79, 'test_iwdr_permutations'), 'keywords': {'test_iwdr_permutations': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'failed', 'longrepr': {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 'lineno': 132, 'message': 'assert 1 == 0'}, 'reprtraceback': {'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_iwdr_permutations(tmp_path_factory: Any) -> None:', ' misc = tmp_path_factory.mktemp("misc")', ' fifth = misc / "fifth"', ' fifth.mkdir()', ' sixth = misc / "sixth"', ' sixth.mkdir()', ' seventh = misc / "seventh"', ' seventh.mkdir()', ' eighth = misc / "eighth"', ' eighth.mkdir()', ' first = misc / "first"', ' first.touch()', ' second = misc / "second"', ' second.touch()', ' third = misc / "third"', ' third.touch()', ' fourth = misc / "fourth"', ' fourth.touch()', ' eleventh = misc / "eleventh"', ' eleventh.touch()', ' twelfth = misc / "twelfth"', ' twelfth.touch()', ' outdir = str(tmp_path_factory.mktemp("outdir"))', ' err_code, stdout, _ = get_main_output(', ' [', ' "--outdir",', ' outdir,', ' "--debug",', ' get_data("tests/wf/iwdr_permutations.cwl"),', ' "--first",', ' str(first),', ' "--second",', ' str(second),', ' "--third",', ' str(third),', ' "--fourth",', ' str(fourth),', ' "--fifth",', ' str(fifth),', ' "--sixth",', ' str(sixth),', ' "--seventh",', ' str(seventh),', ' "--eighth",', ' str(eighth),', ' "--eleventh",', ' str(eleventh),', ' "--eleventh",', ' str(twelfth),', ' ]', ' )', '> assert err_code == 0', 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path_factory', "TempPathFactory(_given_basetemp=PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/.../8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4'), _retention_count=3, _retention_policy='all')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_iwdr.py', 'lineno': 132, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, 'sections': [], 'chain': [({'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_iwdr_permutations(tmp_path_factory: Any) -> None:', ' misc = tmp_path_factory.mktemp("misc")', ' fifth = misc / "fifth"', ' fifth.mkdir()', ' sixth = misc / "sixth"', ' sixth.mkdir()', ' seventh = misc / "seventh"', ' seventh.mkdir()', ' eighth = misc / "eighth"', ' eighth.mkdir()', ' first = misc / "first"', ' first.touch()', ' second = misc / "second"', ' second.touch()', ' third = misc / "third"', ' third.touch()', ' fourth = misc / "fourth"', ' fourth.touch()', ' eleventh = misc / "eleventh"', ' eleventh.touch()', ' twelfth = misc / "twelfth"', ' twelfth.touch()', ' outdir = str(tmp_path_factory.mktemp("outdir"))', ' err_code, stdout, _ = get_main_output(', ' [', ' "--outdir",', ' outdir,', ' "--debug",', ' get_data("tests/wf/iwdr_permutations.cwl"),', ' "--first",', ' str(first),', ' "--second",', ' str(second),', ' "--third",', ' str(third),', ' "--fourth",', ' str(fourth),', ' "--fifth",', ' str(fifth),', ' "--sixth",', ' str(sixth),', ' "--seventh",', ' str(seventh),', ' "--eighth",', ' str(eighth),', ' "--eleventh",', ' str(eleventh),', ' "--eleventh",', ' str(twelfth),', ' ]', ' )', '> assert err_code == 0', 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path_factory', "TempPathFactory(_given_basetemp=PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/.../8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4'), _retention_count=3, _retention_policy='all')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_iwdr.py', 'lineno': 132, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, {'path': '/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 'lineno': 132, 'message': 'assert 1 == 0'}, None)]}, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\'\nDEBUG cwltool:main.py:463 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"file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth",\n "/my_other_path/eighth_read_only_directory",\n "Directory",\n true\n ],\n "_:631d8639-cc11-4787-9f3d-48b57039c0a6": [\n "_:631d8639-cc11-4787-9f3d-48b57039c0a6",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "_:5cd11e38-0800-4f65-ae18-9082ec81cb93": [\n "_:5cd11e38-0800-4f65-ae18-9082ec81cb93",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh",\n "/GbFKKR/eleventh",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth",\n "/GbFKKR/twelfth",\n "File",\n true\n ],\n "_:97279cd1-e7c6-4935-80a6-4f84eeccac8f": [\n "baz",\n "/my_path/my_file_literal",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations.cwl] /private/tmp/docker_tmp_w3qy9tv$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_w3qy9tv,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpxys67wcx,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second,target=/GbFKKR/second_read_only_file,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpws1207gg/third,target=/my_path/third_writable_file \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth,target=/my_other_path/fourth_read_only_file,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth,target=/GbFKKR/sixth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmp073wgswq/seventh,target=/my_path/seventh_writable_directory \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth,target=/my_other_path/eighth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpy0u8j74x/tenth_writable_directory_literal,target=/my_path/tenth_writable_directory_literal \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh,target=/GbFKKR/eleventh,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth,target=/GbFKKR/twelfth,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmps1fmotdc/my_file_literal,target=/my_path/my_file_literal,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpgl_ulo2z/20230605095032-664292.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n --env=LC_ALL=C \\\n docker.io/debian:stable-slim \\\n bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\necho "a" > first_writable_file\necho "b" > /my_path/third_writable_file\ntouch fifth_writable_directory/c\ntouch /my_path/seventh_writable_directory/d\nfind . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\n\' > /private/tmp/docker_tmp_w3qy9tv/log.txt\nINFO cwltool:job.py:905 [job iwdr_permutations.cwl] Max memory used: 0MiB\nERROR cwltool:job.py:395 Exception while running job\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 373, in _execute\n relink_initialworkdir(\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 103, in relink_initialworkdir\n shutil.rmtree(host_outdir_tgt)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 731, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 729, in rmtree\n os.rmdir(path)\nPermissionError: [Errno 13] Permission denied: \'/private/tmp/docker_tmp_w3qy9tv/sixth_read_only_directory\'\nWARNING cwltool:job.py:417 [job iwdr_permutations.cwl] completed permanentFail\nDEBUG cwltool:job.py:422 [job iwdr_permutations.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr_permutations.cwl] Removing input staging directory /private/tmp/docker_tmp9bhpnx_4\nDEBUG cwltool:job.py:454 [job iwdr_permutations.cwl] Removing temporary directory /private/tmp/docker_tmpxys67wcx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_w3qy9tv\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 1.8349911279992739, 'start': 1685951431.870146, 'stop': 1685951433.7050948, '$report_type': 'TestReport', 'item_index': 396, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations', 'location': ('tests/test_iwdr.py', 79, 'test_iwdr_permutations'), 'keywords': {'test_iwdr_permutations': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl",\n "eighth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth"\n },\n "eleventh": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth"\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first"\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second"\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth"\n },\n "tenth": {\n "class": "Directory",\n "basename": "bar",\n "listing": []\n },\n "third": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr_permutations.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr_permutations.cwl] {\n "eighth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth",\n "basename": "eighth"\n },\n "eleventh": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh",\n "size": 0,\n "basename": "eleventh",\n "nameroot": "eleventh",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth",\n "size": 0,\n "basename": "twelfth",\n "nameroot": "twelfth",\n "nameext": ""\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth",\n "size": 0,\n "basename": "fourth",\n "nameroot": "fourth",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:631d8639-cc11-4787-9f3d-48b57039c0a6"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh",\n "basename": "seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth",\n "basename": "sixth"\n },\n "tenth": {\n "class": "Directory",\n "basename": "bar",\n "listing": [],\n "location": "_:5cd11e38-0800-4f65-ae18-9082ec81cb93"\n },\n "third": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third",\n "size": 0,\n "basename": "third",\n "nameroot": "third",\n "nameext": ""\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr_permutations.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth",\n "/my_other_path/eighth_read_only_directory",\n "Directory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh",\n "/GbFKKR/eleventh",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth",\n "/GbFKKR/twelfth",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n false\n ],\n "_:631d8639-cc11-4787-9f3d-48b57039c0a6": [\n "_:631d8639-cc11-4787-9f3d-48b57039c0a6",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second",\n "/GbFKKR/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth",\n "/GbFKKR/sixth_read_only_directory",\n "Directory",\n false\n ],\n "_:5cd11e38-0800-4f65-ae18-9082ec81cb93": [\n "_:5cd11e38-0800-4f65-ae18-9082ec81cb93",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third",\n "/my_path/third_writable_file",\n "WritableFile",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr_permutations.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\necho \\"a\\" > first_writable_file\\necho \\"b\\" > /my_path/third_writable_file\\ntouch fifth_writable_directory/c\\ntouch /my_path/seventh_writable_directory/d\\nfind . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\n"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr_permutations.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second",\n "/GbFKKR/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third",\n "/my_path/third_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth",\n "/GbFKKR/sixth_read_only_directory",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth",\n "/my_other_path/eighth_read_only_directory",\n "Directory",\n true\n ],\n "_:631d8639-cc11-4787-9f3d-48b57039c0a6": [\n "_:631d8639-cc11-4787-9f3d-48b57039c0a6",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "_:5cd11e38-0800-4f65-ae18-9082ec81cb93": [\n "_:5cd11e38-0800-4f65-ae18-9082ec81cb93",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh",\n "/GbFKKR/eleventh",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth",\n "/GbFKKR/twelfth",\n "File",\n true\n ],\n "_:97279cd1-e7c6-4935-80a6-4f84eeccac8f": [\n "baz",\n "/my_path/my_file_literal",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations.cwl] /private/tmp/docker_tmp_w3qy9tv$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_w3qy9tv,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpxys67wcx,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second,target=/GbFKKR/second_read_only_file,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpws1207gg/third,target=/my_path/third_writable_file \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth,target=/my_other_path/fourth_read_only_file,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth,target=/GbFKKR/sixth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmp073wgswq/seventh,target=/my_path/seventh_writable_directory \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth,target=/my_other_path/eighth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpy0u8j74x/tenth_writable_directory_literal,target=/my_path/tenth_writable_directory_literal \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh,target=/GbFKKR/eleventh,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth,target=/GbFKKR/twelfth,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmps1fmotdc/my_file_literal,target=/my_path/my_file_literal,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpgl_ulo2z/20230605095032-664292.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n --env=LC_ALL=C \\\n docker.io/debian:stable-slim \\\n bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\necho "a" > first_writable_file\necho "b" > /my_path/third_writable_file\ntouch fifth_writable_directory/c\ntouch /my_path/seventh_writable_directory/d\nfind . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\n\' > /private/tmp/docker_tmp_w3qy9tv/log.txt\nINFO cwltool:job.py:905 [job iwdr_permutations.cwl] Max memory used: 0MiB\nERROR cwltool:job.py:395 Exception while running job\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 373, in _execute\n relink_initialworkdir(\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 103, in relink_initialworkdir\n shutil.rmtree(host_outdir_tgt)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 731, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 729, in rmtree\n os.rmdir(path)\nPermissionError: [Errno 13] Permission denied: \'/private/tmp/docker_tmp_w3qy9tv/sixth_read_only_directory\'\nWARNING cwltool:job.py:417 [job iwdr_permutations.cwl] completed permanentFail\nDEBUG cwltool:job.py:422 [job iwdr_permutations.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr_permutations.cwl] Removing input staging directory /private/tmp/docker_tmp9bhpnx_4\nDEBUG cwltool:job.py:454 [job iwdr_permutations.cwl] Removing temporary directory /private/tmp/docker_tmpxys67wcx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_w3qy9tv\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.001088491000700742, 'start': 1685951433.917353, 'stop': 1685951433.918443, '$report_type': 'TestReport', 'item_index': 396, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_iwdr.py::test_iwdr_permutations + location: ('tests/test_iwdr.py', 79, 'test_iwdr_permutations') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_iwdr.py::test_iwdr_permutations_readonly + location: ('tests/test_iwdr.py', 138, 'test_iwdr_permutations_readonly') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_readonly', 'location': ('tests/test_iwdr.py', 138, 'test_iwdr_permutations_readonly'), 'keywords': {'test_iwdr_permutations_readonly': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003601219996198779, 'start': 1685951433.9202828, 'stop': 1685951433.920644, '$report_type': 'TestReport', 'item_index': 397, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment_from_packed', 'location': ('tests/test_load_tool.py', 83, 'test_load_graph_fragment_from_packed'), 'keywords': {'test_load_graph_fragment_from_packed': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.9820490420006536, 'start': 1685951433.286717, 'stop': 1685951434.2687428, '$report_type': 'TestReport', 'item_index': 414, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment_from_packed', 'location': ('tests/test_load_tool.py', 83, 'test_load_graph_fragment_from_packed'), 'keywords': {'test_load_graph_fragment_from_packed': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002711429997361847, 'start': 1685951434.269431, 'stop': 1685951434.2697039, '$report_type': 'TestReport', 'item_index': 414, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_load_tool.py::test_load_graph_fragment_from_packed + location: ('tests/test_load_tool.py', 83, 'test_load_graph_fragment_from_packed') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_load_tool.py::test_import_tracked + location: ('tests/test_load_tool.py', 130, 'test_import_tracked') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_import_tracked', 'location': ('tests/test_load_tool.py', 130, 'test_import_tracked'), 'keywords': {'test_import_tracked': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002453380002407357, 'start': 1685951434.270707, 'stop': 1685951434.270954, '$report_type': 'TestReport', 'item_index': 415, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_readonly', 'location': ('tests/test_iwdr.py', 138, 'test_iwdr_permutations_readonly'), 'keywords': {'test_iwdr_permutations_readonly': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "basename": "sixth_read_only_directory",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/second_read_only_file",\n "basename": "second_read_only_file",\n "path": "/private/tmp/docker_tmpp5625vra/second_read_only_file"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/first_writable_file",\n "basename": "first_writable_file",\n "path": "/private/tmp/docker_tmpp5625vra/first_writable_file"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "basename": "fifth_writable_directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/foo",\n "basename": "foo",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/foo"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/bar",\n "basename": "bar",\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/bar"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/c",\n "basename": "c",\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/c"\n }\n ],\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "basename": "nineth_writable_directory_literal",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal"\n }\n ],\n "path": "/private/tmp/docker_tmpp5625vra"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl",\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] {\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:1f56c615-53c2-403e-b9c7-4924d21f8b70"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "basename": "sixth0"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n false\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\necho \\"a\\" > first_writable_file\\ntouch fifth_writable_directory/c\\n"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n true\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job iwdr_permutations_nocontainer.cwl] /private/tmp/docker_tmpp5625vra$ bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\necho "a" > first_writable_file\ntouch fifth_writable_directory/c\n\'\n.\n./fifth_writable_directory\n./fifth_writable_directory/bar\n./fifth_writable_directory/foo\n./first_writable_file\n./nineth_writable_directory_literal\n./second_read_only_file\n./sixth_read_only_directory\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job iwdr_permutations_nocontainer.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "nameroot": "docker_tmpp5625vra",\n "nameext": "",\n "class": "Directory"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] Removing input staging directory /private/tmp/docker_tmpjhjm2onk\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] Removing temporary directory /private/tmp/docker_tmpk21vv0i5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpp5625vra\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl",\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr_permutations_nocontainer.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr_permutations_nocontainer.cwl] {\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:1f56c615-53c2-403e-b9c7-4924d21f8b70"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "basename": "sixth0"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr_permutations_nocontainer.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n false\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr_permutations_nocontainer.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\necho \\"a\\" > first_writable_file\\ntouch fifth_writable_directory/c\\n"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr_permutations_nocontainer.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n true\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations_nocontainer.cwl] /private/tmp/docker_tmpp5625vra$ bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\necho "a" > first_writable_file\ntouch fifth_writable_directory/c\n\'\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr_permutations_nocontainer.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr_permutations_nocontainer.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "nameroot": "docker_tmpp5625vra",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job iwdr_permutations_nocontainer.cwl] Removing input staging directory /private/tmp/docker_tmpjhjm2onk\nDEBUG cwltool:job.py:454 [job iwdr_permutations_nocontainer.cwl] Removing temporary directory /private/tmp/docker_tmpk21vv0i5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp5625vra\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.8987138219999906, 'start': 1685951433.9209988, 'stop': 1685951434.819693, '$report_type': 'TestReport', 'item_index': 397, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_readonly', 'location': ('tests/test_iwdr.py', 138, 'test_iwdr_permutations_readonly'), 'keywords': {'test_iwdr_permutations_readonly': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "basename": "sixth_read_only_directory",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/second_read_only_file",\n "basename": "second_read_only_file",\n "path": "/private/tmp/docker_tmpp5625vra/second_read_only_file"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/first_writable_file",\n "basename": "first_writable_file",\n "path": "/private/tmp/docker_tmpp5625vra/first_writable_file"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "basename": "fifth_writable_directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/foo",\n "basename": "foo",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/foo"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/bar",\n "basename": "bar",\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/bar"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/c",\n "basename": "c",\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/c"\n }\n ],\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "basename": "nineth_writable_directory_literal",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal"\n }\n ],\n "path": "/private/tmp/docker_tmpp5625vra"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl",\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] {\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:1f56c615-53c2-403e-b9c7-4924d21f8b70"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "basename": "sixth0"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n false\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\necho \\"a\\" > first_writable_file\\ntouch fifth_writable_directory/c\\n"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n true\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job iwdr_permutations_nocontainer.cwl] /private/tmp/docker_tmpp5625vra$ bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\necho "a" > first_writable_file\ntouch fifth_writable_directory/c\n\'\n.\n./fifth_writable_directory\n./fifth_writable_directory/bar\n./fifth_writable_directory/foo\n./first_writable_file\n./nineth_writable_directory_literal\n./second_read_only_file\n./sixth_read_only_directory\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job iwdr_permutations_nocontainer.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "nameroot": "docker_tmpp5625vra",\n "nameext": "",\n "class": "Directory"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] Removing input staging directory /private/tmp/docker_tmpjhjm2onk\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] Removing temporary directory /private/tmp/docker_tmpk21vv0i5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpp5625vra\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl",\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr_permutations_nocontainer.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr_permutations_nocontainer.cwl] {\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:1f56c615-53c2-403e-b9c7-4924d21f8b70"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "basename": "sixth0"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr_permutations_nocontainer.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n false\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr_permutations_nocontainer.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\necho \\"a\\" > first_writable_file\\ntouch fifth_writable_directory/c\\n"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr_permutations_nocontainer.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n true\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations_nocontainer.cwl] /private/tmp/docker_tmpp5625vra$ bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\necho "a" > first_writable_file\ntouch fifth_writable_directory/c\n\'\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr_permutations_nocontainer.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr_permutations_nocontainer.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "nameroot": "docker_tmpp5625vra",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job iwdr_permutations_nocontainer.cwl] Removing input staging directory /private/tmp/docker_tmpjhjm2onk\nDEBUG cwltool:job.py:454 [job iwdr_permutations_nocontainer.cwl] Removing temporary directory /private/tmp/docker_tmpk21vv0i5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp5625vra\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00042286200005037244, 'start': 1685951434.821234, 'stop': 1685951434.8216588, '$report_type': 'TestReport', 'item_index': 397, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_iwdr.py::test_iwdr_permutations_readonly + location: ('tests/test_iwdr.py', 138, 'test_iwdr_permutations_readonly') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_inplace', 'location': ('tests/test_iwdr.py', 188, 'test_iwdr_permutations_inplace'), 'keywords': {'test_iwdr_permutations_inplace': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005866809997314704, 'start': 1685951434.8234959, 'stop': 1685951434.824085, '$report_type': 'TestReport', 'item_index': 398, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_iwdr.py::test_iwdr_permutations_inplace + location: ('tests/test_iwdr.py', 188, 'test_iwdr_permutations_inplace') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[]'), 'keywords': {'test_cache_relative_paths[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmpu4gvxfws/stg543c1c83-2e8e-49d1-86fa-ec758f66c2ba/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmpu4gvxfws/stg543c1c83-2e8e-49d1-86fa-ec758f66c2ba/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job secondary-files.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl] Removing input staging directory /private/tmp/docker_tmpu4gvxfws\nDEBUG cwltool:job.py:454 [job secondary-files.cwl] Removing temporary directory /private/tmp/docker_tmpk1mp264l\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cacheckg89j70\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_2] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_2] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cachee9f67smd\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.106250634999924, 'start': 1685951432.897739, 'stop': 1685951435.003938, '$report_type': 'TestReport', 'item_index': 300, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[]'), 'keywords': {'test_cache_relative_paths[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmpu4gvxfws/stg543c1c83-2e8e-49d1-86fa-ec758f66c2ba/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmpu4gvxfws/stg543c1c83-2e8e-49d1-86fa-ec758f66c2ba/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job secondary-files.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl] Removing input staging directory /private/tmp/docker_tmpu4gvxfws\nDEBUG cwltool:job.py:454 [job secondary-files.cwl] Removing temporary directory /private/tmp/docker_tmpk1mp264l\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cacheckg89j70\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_2] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_2] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cachee9f67smd\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005469789994094754, 'start': 1685951435.004695, 'stop': 1685951435.0052428, '$report_type': 'TestReport', 'item_index': 300, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cache_relative_paths[] + location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cache_relative_paths[--parallel] + location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel]'), 'keywords': {'test_cache_relative_paths[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0020195979996060487, 'start': 1685951435.007218, 'stop': 1685951435.0092402, '$report_type': 'TestReport', 'item_index': 301, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_import_tracked', 'location': ('tests/test_load_tool.py', 130, 'test_import_tracked'), 'keywords': {'test_import_tracked': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:34]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl'\n\x1b[32m[2023-06-05 09:50:35]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811.cwl'")], 'duration': 1.5744697370000722, 'start': 1685951434.271424, 'stop': 1685951435.845856, '$report_type': 'TestReport', 'item_index': 415, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_import_tracked', 'location': ('tests/test_load_tool.py', 130, 'test_import_tracked'), 'keywords': {'test_import_tracked': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:34]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl'\n\x1b[32m[2023-06-05 09:50:35]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811.cwl'")], 'duration': 0.00018237499989481876, 'start': 1685951435.846292, 'stop': 1685951435.8464751, '$report_type': 'TestReport', 'item_index': 415, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_load_tool.py::test_import_tracked + location: ('tests/test_load_tool.py', 130, 'test_import_tracked') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_load_tool.py::test_load_badhints + location: ('tests/test_load_tool.py', 148, 'test_load_badhints') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints', 'location': ('tests/test_load_tool.py', 148, 'test_load_badhints'), 'keywords': {'test_load_badhints': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00018566800008557038, 'start': 1685951435.8474848, 'stop': 1685951435.847672, '$report_type': 'TestReport', 'item_index': 416, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints', 'location': ('tests/test_load_tool.py', 148, 'test_load_badhints'), 'keywords': {'test_load_badhints': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.02006813099978899, 'start': 1685951435.847969, 'stop': 1685951435.868038, '$report_type': 'TestReport', 'item_index': 416, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints', 'location': ('tests/test_load_tool.py', 148, 'test_load_badhints'), 'keywords': {'test_load_badhints': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00018017899947153637, 'start': 1685951435.868441, 'stop': 1685951435.868622, '$report_type': 'TestReport', 'item_index': 416, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_load_tool.py::test_load_badhints + location: ('tests/test_load_tool.py', 148, 'test_load_badhints') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_load_tool.py::test_load_badhints_nodict + location: ('tests/test_load_tool.py', 159, 'test_load_badhints_nodict') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints_nodict', 'location': ('tests/test_load_tool.py', 159, 'test_load_badhints_nodict'), 'keywords': {'test_load_badhints_nodict': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0001881380003396771, 'start': 1685951435.869579, 'stop': 1685951435.869768, '$report_type': 'TestReport', 'item_index': 417, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints_nodict', 'location': ('tests/test_load_tool.py', 159, 'test_load_badhints_nodict'), 'keywords': {'test_load_badhints_nodict': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.019618063000052643, 'start': 1685951435.870068, 'stop': 1685951435.889687, '$report_type': 'TestReport', 'item_index': 417, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints_nodict', 'location': ('tests/test_load_tool.py', 159, 'test_load_badhints_nodict'), 'keywords': {'test_load_badhints_nodict': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00021258099968690658, 'start': 1685951435.8901, 'stop': 1685951435.890314, '$report_type': 'TestReport', 'item_index': 417, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_load_tool.py::test_load_badhints_nodict + location: ('tests/test_load_tool.py', 159, 'test_load_badhints_nodict') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_loop_with_all_output_method + location: ('tests/test_loop.py', 161, 'test_loop_with_all_output_method') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method', 'location': ('tests/test_loop.py', 161, 'test_loop_with_all_output_method'), 'keywords': {'test_loop_with_all_output_method': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002493149995643762, 'start': 1685951435.891244, 'stop': 1685951435.8914938, '$report_type': 'TestReport', 'item_index': 432, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_dir[--debug]', 'location': ('tests/test_examples.py', 1084, 'test_cid_file_dir[--debug]'), 'keywords': {'test_cid_file_dir[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_3\nDEBUG cwltool:workflow_job.py:727 [step task2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_3] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_3\nDEBUG cwltool:command_line_tool.py:988 [job task2_3] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_3] initial work dir {}\nINFO cwltool:job.py:266 [job task2_3] /private/tmp/docker_tmp1nnhk1t7$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp1nnhk1t7,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmpod5r_84n,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_cid_file_dir___debug_0/20230605095034-025713.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_3] completed success\nDEBUG cwltool:job.py:422 [job task2_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1nnhk1t7/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_3] completed success\nDEBUG cwltool:job.py:446 [job task2_3] Removing input staging directory /private/tmp/docker_tmpwq9_h_7z\nDEBUG cwltool:job.py:454 [job task2_3] Removing temporary directory /private/tmp/docker_tmpod5r_84n\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_3\nDEBUG cwltool:workflow_job.py:727 [step task1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_3\nDEBUG cwltool:command_line_tool.py:988 [job task1_3] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_3] initial work dir {}\nINFO cwltool:job.py:266 [job task1_3] /private/tmp/docker_tmpudmds_on$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpudmds_on,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmpa5phkv0m,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_cid_file_dir___debug_0/20230605095035-063346.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_3] completed success\nDEBUG cwltool:job.py:422 [job task1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpudmds_on/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_3] Removing input staging directory /private/tmp/docker_tmp_be0w_8a\nDEBUG cwltool:job.py:454 [job task1_3] Removing temporary directory /private/tmp/docker_tmpa5phkv0m\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1nnhk1t7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpudmds_on\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwhodp045\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 3.749131440000383, 'start': 1685951432.337434, 'stop': 1685951436.086473, '$report_type': 'TestReport', 'item_index': 266, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_dir[--debug]', 'location': ('tests/test_examples.py', 1084, 'test_cid_file_dir[--debug]'), 'keywords': {'test_cid_file_dir[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_3\nDEBUG cwltool:workflow_job.py:727 [step task2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_3] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_3\nDEBUG cwltool:command_line_tool.py:988 [job task2_3] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_3] initial work dir {}\nINFO cwltool:job.py:266 [job task2_3] /private/tmp/docker_tmp1nnhk1t7$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp1nnhk1t7,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmpod5r_84n,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_cid_file_dir___debug_0/20230605095034-025713.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_3] completed success\nDEBUG cwltool:job.py:422 [job task2_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1nnhk1t7/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_3] completed success\nDEBUG cwltool:job.py:446 [job task2_3] Removing input staging directory /private/tmp/docker_tmpwq9_h_7z\nDEBUG cwltool:job.py:454 [job task2_3] Removing temporary directory /private/tmp/docker_tmpod5r_84n\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_3\nDEBUG cwltool:workflow_job.py:727 [step task1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_3\nDEBUG cwltool:command_line_tool.py:988 [job task1_3] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_3] initial work dir {}\nINFO cwltool:job.py:266 [job task1_3] /private/tmp/docker_tmpudmds_on$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpudmds_on,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmpa5phkv0m,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_cid_file_dir___debug_0/20230605095035-063346.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_3] completed success\nDEBUG cwltool:job.py:422 [job task1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpudmds_on/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_3] Removing input staging directory /private/tmp/docker_tmp_be0w_8a\nDEBUG cwltool:job.py:454 [job task1_3] Removing temporary directory /private/tmp/docker_tmpa5phkv0m\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1nnhk1t7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpudmds_on\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwhodp045\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005957659996056464, 'start': 1685951436.0874019, 'stop': 1685951436.0879989, '$report_type': 'TestReport', 'item_index': 266, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_dir[--debug] + location: ('tests/test_examples.py', 1084, 'test_cid_file_dir[--debug]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_validate_loop + location: ('tests/test_loop.py', 10, 'test_validate_loop') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop', 'location': ('tests/test_loop.py', 10, 'test_validate_loop'), 'keywords': {'test_validate_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00019735000023501925, 'start': 1685951436.0892, 'stop': 1685951436.089399, '$report_type': 'TestReport', 'item_index': 418, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method', 'location': ('tests/test_loop.py', 161, 'test_loop_with_all_output_method'), 'keywords': {'test_loop_with_all_output_method': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/all-output-loop.cwl:25:7: object id 'tests/loop/all-output-loop.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _6] start\n\x1b[1;30mINFO\x1b[0m [workflow _6] starting step subworkflow\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _6] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/all-output-loop.cwl:25:7: object id \'tests/loop/all-output-loop.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _6] start\nDEBUG cwltool:workflow_job.py:777 [workflow _6] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _6] starting step subworkflow\nDEBUG cwltool:workflow_job.py:727 [step subworkflow] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow] inputs was {\n "i1": 10\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": [\n 2,\n 3,\n 4,\n 5,\n 6,\n 7,\n 8,\n 9,\n 10\n ]\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow] completed success\nINFO cwltool:workflow_job.py:539 [workflow _6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _6] outputs {\n "o1": [\n 2,\n 3,\n 4,\n 5,\n 6,\n 7,\n 8,\n 9,\n 10\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptip_9h3h\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.8467874959997062, 'start': 1685951435.892153, 'stop': 1685951436.738921, '$report_type': 'TestReport', 'item_index': 432, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method', 'location': ('tests/test_loop.py', 161, 'test_loop_with_all_output_method'), 'keywords': {'test_loop_with_all_output_method': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/all-output-loop.cwl:25:7: object id 'tests/loop/all-output-loop.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _6] start\n\x1b[1;30mINFO\x1b[0m [workflow _6] starting step subworkflow\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _6] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/all-output-loop.cwl:25:7: object id \'tests/loop/all-output-loop.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _6] start\nDEBUG cwltool:workflow_job.py:777 [workflow _6] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _6] starting step subworkflow\nDEBUG cwltool:workflow_job.py:727 [step subworkflow] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow] inputs was {\n "i1": 10\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": [\n 2,\n 3,\n 4,\n 5,\n 6,\n 7,\n 8,\n 9,\n 10\n ]\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow] completed success\nINFO cwltool:workflow_job.py:539 [workflow _6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _6] outputs {\n "o1": [\n 2,\n 3,\n 4,\n 5,\n 6,\n 7,\n 8,\n 9,\n 10\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptip_9h3h\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0003319159995953669, 'start': 1685951436.7396128, 'stop': 1685951436.739947, '$report_type': 'TestReport', 'item_index': 432, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_loop_with_all_output_method + location: ('tests/test_loop.py', 161, 'test_loop_with_all_output_method') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_loop_with_all_output_method_no_iteration + location: ('tests/test_loop.py', 174, 'test_loop_with_all_output_method_no_iteration') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method_no_iteration', 'location': ('tests/test_loop.py', 174, 'test_loop_with_all_output_method_no_iteration'), 'keywords': {'test_loop_with_all_output_method_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002555680002842564, 'start': 1685951436.74208, 'stop': 1685951436.742337, '$report_type': 'TestReport', 'item_index': 433, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel]'), 'keywords': {'test_cache_relative_paths[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_3] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_3] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_3] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_3] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmpbsfowjeo/stg9c3282a7-e9fe-48f9-b429-4885d74af651/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmpbsfowjeo/stg9c3282a7-e9fe-48f9-b429-4885d74af651/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(secondary-files.cwl_3), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job secondary-files.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_3] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_3] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_3] Removing input staging directory /private/tmp/docker_tmpbsfowjeo\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_3] Removing temporary directory /private/tmp/docker_tmpxeztwk4m\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache483lpwnx\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_4] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_4] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cacheyc1ic0v7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.8110991969997485, 'start': 1685951435.009705, 'stop': 1685951436.8207622, '$report_type': 'TestReport', 'item_index': 301, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel]'), 'keywords': {'test_cache_relative_paths[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_3] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_3] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_3] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_3] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmpbsfowjeo/stg9c3282a7-e9fe-48f9-b429-4885d74af651/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmpbsfowjeo/stg9c3282a7-e9fe-48f9-b429-4885d74af651/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(secondary-files.cwl_3), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job secondary-files.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_3] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_3] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_3] Removing input staging directory /private/tmp/docker_tmpbsfowjeo\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_3] Removing temporary directory /private/tmp/docker_tmpxeztwk4m\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache483lpwnx\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_4] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_4] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cacheyc1ic0v7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007077919999574078, 'start': 1685951436.821831, 'stop': 1685951436.82254, '$report_type': 'TestReport', 'item_index': 301, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cache_relative_paths[--parallel] + location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cache_relative_paths[--debug] + location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--debug]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--debug]'), 'keywords': {'test_cache_relative_paths[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016138500004672096, 'start': 1685951436.824117, 'stop': 1685951436.8257332, '$report_type': 'TestReport', 'item_index': 302, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_require_prefix_timelimit', 'location': ('tests/test_ext.py', 258, 'test_require_prefix_timelimit'), 'keywords': {'test_require_prefix_timelimit': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl'\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] /private/tmp/docker_tmp58pbn2k5$ sleep \\\n 3\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] Max memory used: 1MiB\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/timelimit.cwl:12:1: checking field 'requirements'\ntests/wf/timelimit.cwl:13:3: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#TimeLimit'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl'\n\x1b[1;30mINFO\x1b[0m [job timelimit-fail.cwl] /private/tmp/docker_tmpn6zcewj2$ sleep \\\n 5\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] exceeded time limit of 3 seconds and will be terminated\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job timelimit-fail.cwl] Max memory used: 1MiB\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] was terminated by signal: SIGTERM\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] completed permanentFail\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl",\n "sleep_time": 3\n}\nDEBUG cwltool:command_line_tool.py:982 [job timelimit.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\nDEBUG cwltool:command_line_tool.py:988 [job timelimit.cwl] {\n "sleep_time": 3\n}\nDEBUG cwltool:command_line_tool.py:1000 [job timelimit.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job timelimit.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sleep"\n },\n {\n "position": [\n 0,\n "sleep_time"\n ],\n "datum": 3\n }\n]\nDEBUG cwltool:job.py:215 [job timelimit.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job timelimit.cwl] /private/tmp/docker_tmp58pbn2k5$ sleep \\\n 3\nINFO cwltool:job.py:532 [job timelimit.cwl] Max memory used: 1MiB\nINFO cwltool:job.py:419 [job timelimit.cwl] completed success\nDEBUG cwltool:job.py:422 [job timelimit.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job timelimit.cwl] Removing input staging directory /private/tmp/docker_tmpettflfps\nDEBUG cwltool:job.py:454 [job timelimit.cwl] Removing temporary directory /private/tmp/docker_tmpfantbkdr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp58pbn2k5\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/timelimit.cwl:12:1: checking field \'requirements\'\ntests/wf/timelimit.cwl:13:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#TimeLimit\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job timelimit-fail.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\nDEBUG cwltool:command_line_tool.py:988 [job timelimit-fail.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job timelimit-fail.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job timelimit-fail.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sleep"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "5"\n }\n]\nDEBUG cwltool:job.py:215 [job timelimit-fail.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job timelimit-fail.cwl] /private/tmp/docker_tmpn6zcewj2$ sleep \\\n 5\nWARNING cwltool:job.py:967 [job timelimit-fail.cwl] exceeded time limit of 3 seconds and will be terminated\nINFO cwltool:job.py:532 [job timelimit-fail.cwl] Max memory used: 1MiB\nWARNING cwltool:job.py:363 [job timelimit-fail.cwl] was terminated by signal: SIGTERM\nWARNING cwltool:job.py:417 [job timelimit-fail.cwl] completed permanentFail\nDEBUG cwltool:job.py:422 [job timelimit-fail.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job timelimit-fail.cwl] Removing input staging directory /private/tmp/docker_tmpt1wowho0\nDEBUG cwltool:job.py:454 [job timelimit-fail.cwl] Removing temporary directory /private/tmp/docker_tmp8knp65by\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpn6zcewj2\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 8.512694676000137, 'start': 1685951428.474015, 'stop': 1685951436.986499, '$report_type': 'TestReport', 'item_index': 378, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_require_prefix_timelimit', 'location': ('tests/test_ext.py', 258, 'test_require_prefix_timelimit'), 'keywords': {'test_require_prefix_timelimit': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl'\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] /private/tmp/docker_tmp58pbn2k5$ sleep \\\n 3\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] Max memory used: 1MiB\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/timelimit.cwl:12:1: checking field 'requirements'\ntests/wf/timelimit.cwl:13:3: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#TimeLimit'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl'\n\x1b[1;30mINFO\x1b[0m [job timelimit-fail.cwl] /private/tmp/docker_tmpn6zcewj2$ sleep \\\n 5\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] exceeded time limit of 3 seconds and will be terminated\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job timelimit-fail.cwl] Max memory used: 1MiB\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] was terminated by signal: SIGTERM\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] completed permanentFail\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl",\n "sleep_time": 3\n}\nDEBUG cwltool:command_line_tool.py:982 [job timelimit.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\nDEBUG cwltool:command_line_tool.py:988 [job timelimit.cwl] {\n "sleep_time": 3\n}\nDEBUG cwltool:command_line_tool.py:1000 [job timelimit.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job timelimit.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sleep"\n },\n {\n "position": [\n 0,\n "sleep_time"\n ],\n "datum": 3\n }\n]\nDEBUG cwltool:job.py:215 [job timelimit.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job timelimit.cwl] /private/tmp/docker_tmp58pbn2k5$ sleep \\\n 3\nINFO cwltool:job.py:532 [job timelimit.cwl] Max memory used: 1MiB\nINFO cwltool:job.py:419 [job timelimit.cwl] completed success\nDEBUG cwltool:job.py:422 [job timelimit.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job timelimit.cwl] Removing input staging directory /private/tmp/docker_tmpettflfps\nDEBUG cwltool:job.py:454 [job timelimit.cwl] Removing temporary directory /private/tmp/docker_tmpfantbkdr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp58pbn2k5\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/timelimit.cwl:12:1: checking field \'requirements\'\ntests/wf/timelimit.cwl:13:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#TimeLimit\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job timelimit-fail.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\nDEBUG cwltool:command_line_tool.py:988 [job timelimit-fail.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job timelimit-fail.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job timelimit-fail.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sleep"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "5"\n }\n]\nDEBUG cwltool:job.py:215 [job timelimit-fail.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job timelimit-fail.cwl] /private/tmp/docker_tmpn6zcewj2$ sleep \\\n 5\nWARNING cwltool:job.py:967 [job timelimit-fail.cwl] exceeded time limit of 3 seconds and will be terminated\nINFO cwltool:job.py:532 [job timelimit-fail.cwl] Max memory used: 1MiB\nWARNING cwltool:job.py:363 [job timelimit-fail.cwl] was terminated by signal: SIGTERM\nWARNING cwltool:job.py:417 [job timelimit-fail.cwl] completed permanentFail\nDEBUG cwltool:job.py:422 [job timelimit-fail.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job timelimit-fail.cwl] Removing input staging directory /private/tmp/docker_tmpt1wowho0\nDEBUG cwltool:job.py:454 [job timelimit-fail.cwl] Removing temporary directory /private/tmp/docker_tmp8knp65by\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpn6zcewj2\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.000628123000751657, 'start': 1685951436.9878762, 'stop': 1685951436.988506, '$report_type': 'TestReport', 'item_index': 378, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_require_prefix_timelimit + location: ('tests/test_ext.py', 258, 'test_require_prefix_timelimit') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_ext.py::test_warn_large_inputs + location: ('tests/test_ext.py', 264, 'test_warn_large_inputs') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_warn_large_inputs', 'location': ('tests/test_ext.py', 264, 'test_warn_large_inputs'), 'keywords': {'test_warn_large_inputs': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00031238300016411813, 'start': 1685951436.9900942, 'stop': 1685951436.990408, '$report_type': 'TestReport', 'item_index': 379, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop', 'location': ('tests/test_loop.py', 10, 'test_validate_loop'), 'keywords': {'test_validate_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined")], 'duration': 0.9011028020004233, 'start': 1685951436.089872, 'stop': 1685951436.990954, '$report_type': 'TestReport', 'item_index': 418, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop', 'location': ('tests/test_loop.py', 10, 'test_validate_loop'), 'keywords': {'test_validate_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined")], 'duration': 0.000282838999737578, 'start': 1685951436.9915211, 'stop': 1685951436.9918048, '$report_type': 'TestReport', 'item_index': 418, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_validate_loop + location: ('tests/test_loop.py', 10, 'test_validate_loop') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_no_ext + location: ('tests/test_loop.py', 20, 'test_validate_loop_fail_no_ext') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_no_ext', 'location': ('tests/test_loop.py', 20, 'test_validate_loop_fail_no_ext'), 'keywords': {'test_validate_loop_fail_no_ext': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00032370300050388323, 'start': 1685951436.993045, 'stop': 1685951436.9933708, '$report_type': 'TestReport', 'item_index': 419, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug]', 'location': ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]'), 'keywords': {'test_cid_file_non_existing_dir[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task2_9\nDEBUG cwltool:workflow_job.py:727 [step task2_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_9\nDEBUG cwltool:command_line_tool.py:988 [job task2_7] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_7), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task1_9\nDEBUG cwltool:workflow_job.py:727 [step task1_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_9\nDEBUG cwltool:command_line_tool.py:988 [job task1_7] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_7), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_7] initial work dir {}\nDEBUG cwltool:job.py:215 [job task1_7] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:executors.py:430 Workflow cannot make any more progress.\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcznvku2h\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwnjg_83y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa2g7ccv0\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 4.7696697329993185, 'start': 1685951432.718051, 'stop': 1685951437.487604, '$report_type': 'TestReport', 'item_index': 275, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug]', 'location': ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]'), 'keywords': {'test_cid_file_non_existing_dir[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task2_9\nDEBUG cwltool:workflow_job.py:727 [step task2_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_9\nDEBUG cwltool:command_line_tool.py:988 [job task2_7] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_7), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task1_9\nDEBUG cwltool:workflow_job.py:727 [step task1_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_9\nDEBUG cwltool:command_line_tool.py:988 [job task1_7] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_7), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_7] initial work dir {}\nDEBUG cwltool:job.py:215 [job task1_7] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:executors.py:430 Workflow cannot make any more progress.\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcznvku2h\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwnjg_83y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa2g7ccv0\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.0010064870002679527, 'start': 1685951437.488749, 'stop': 1685951437.4897568, '$report_type': 'TestReport', 'item_index': 275, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug] + location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]'), 'keywords': {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016974030004348606, 'start': 1685951437.491211, 'stop': 1685951437.4929101, '$report_type': 'TestReport', 'item_index': 276, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_inplace', 'location': ('tests/test_iwdr.py', 188, 'test_iwdr_permutations_inplace'), 'keywords': {'test_iwdr_permutations_inplace': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'failed', 'longrepr': {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 'lineno': 243, 'message': 'assert 1 == 0'}, 'reprtraceback': {'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_iwdr_permutations_inplace(tmp_path_factory: Any) -> None:', ' misc = tmp_path_factory.mktemp("misc")', ' fifth = misc / "fifth"', ' fifth.mkdir()', ' sixth = misc / "sixth"', ' sixth.mkdir()', ' seventh = misc / "seventh"', ' seventh.mkdir()', ' eighth = misc / "eighth"', ' eighth.mkdir()', ' first = misc / "first"', ' first.touch()', ' second = misc / "second"', ' second.touch()', ' third = misc / "third"', ' third.touch()', ' fourth = misc / "fourth"', ' fourth.touch()', ' eleventh = misc / "eleventh"', ' eleventh.touch()', ' twelfth = misc / "twelfth"', ' twelfth.touch()', ' outdir = str(tmp_path_factory.mktemp("outdir"))', ' err_code, stdout, _ = get_main_output(', ' [', ' "--outdir",', ' outdir,', ' "--enable-ext",', ' "--overrides",', ' get_data("tests/wf/iwdr_permutations_inplace.yml"),', ' get_data("tests/wf/iwdr_permutations.cwl"),', ' "--first",', ' str(first),', ' "--second",', ' str(second),', ' "--third",', ' str(third),', ' "--fourth",', ' str(fourth),', ' "--fifth",', ' str(fifth),', ' "--sixth",', ' str(sixth),', ' "--seventh",', ' str(seventh),', ' "--eighth",', ' str(eighth),', ' "--eleventh",', ' str(eleventh),', ' "--eleventh",', ' str(twelfth),', ' ]', ' )', '> assert err_code == 0', 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path_factory', "TempPathFactory(_given_basetemp=PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/.../8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4'), _retention_count=3, _retention_policy='all')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_iwdr.py', 'lineno': 243, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, 'sections': [], 'chain': [({'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_iwdr_permutations_inplace(tmp_path_factory: Any) -> None:', ' misc = tmp_path_factory.mktemp("misc")', ' fifth = misc / "fifth"', ' fifth.mkdir()', ' sixth = misc / "sixth"', ' sixth.mkdir()', ' seventh = misc / "seventh"', ' seventh.mkdir()', ' eighth = misc / "eighth"', ' eighth.mkdir()', ' first = misc / "first"', ' first.touch()', ' second = misc / "second"', ' second.touch()', ' third = misc / "third"', ' third.touch()', ' fourth = misc / "fourth"', ' fourth.touch()', ' eleventh = misc / "eleventh"', ' eleventh.touch()', ' twelfth = misc / "twelfth"', ' twelfth.touch()', ' outdir = str(tmp_path_factory.mktemp("outdir"))', ' err_code, stdout, _ = get_main_output(', ' [', ' "--outdir",', ' outdir,', ' "--enable-ext",', ' "--overrides",', ' get_data("tests/wf/iwdr_permutations_inplace.yml"),', ' get_data("tests/wf/iwdr_permutations.cwl"),', ' "--first",', ' str(first),', ' "--second",', ' str(second),', ' "--third",', ' str(third),', ' "--fourth",', ' str(fourth),', ' "--fifth",', ' str(fifth),', ' "--sixth",', ' str(sixth),', ' "--seventh",', ' str(seventh),', ' "--eighth",', ' str(eighth),', ' "--eleventh",', ' str(eleventh),', ' "--eleventh",', ' str(twelfth),', ' ]', ' )', '> assert err_code == 0', 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path_factory', "TempPathFactory(_given_basetemp=PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/.../8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4'), _retention_count=3, _retention_policy='all')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_iwdr.py', 'lineno': 243, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, {'path': '/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 'lineno': 243, 'message': 'assert 1 == 0'}, None)]}, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl",\n "eighth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth"\n },\n "eleventh": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth"\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first"\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second"\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth"\n },\n "tenth": {\n "class": "Directory",\n "basename": "bar",\n "listing": []\n },\n "third": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr_permutations.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr_permutations.cwl_2] {\n "eighth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth",\n "basename": "eighth"\n },\n "eleventh": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh",\n "size": 0,\n "basename": "eleventh",\n "nameroot": "eleventh",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "size": 0,\n "basename": "twelfth",\n "nameroot": "twelfth",\n "nameext": ""\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "size": 0,\n "basename": "fourth",\n "nameroot": "fourth",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:0b3439f5-e916-4bb0-875b-01251ced359b"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "basename": "seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "basename": "sixth"\n },\n "tenth": {\n "class": "Directory",\n "basename": "bar",\n "listing": [],\n "location": "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b"\n },\n "third": {\n "class": "File",\n "location": 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"file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "/GbFKKR/twelfth",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n false\n ],\n "_:0b3439f5-e916-4bb0-875b-01251ced359b": [\n "_:0b3439f5-e916-4bb0-875b-01251ced359b",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "/GbFKKR/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "/GbFKKR/sixth_read_only_directory",\n "Directory",\n false\n ],\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b": [\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third",\n "/my_path/third_writable_file",\n "WritableFile",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr_permutations.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\necho \\"a\\" > first_writable_file\\necho \\"b\\" > /my_path/third_writable_file\\ntouch fifth_writable_directory/c\\ntouch /my_path/seventh_writable_directory/d\\nfind . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\n"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr_permutations.cwl_2] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "/GbFKKR/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third",\n "/my_path/third_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "/GbFKKR/sixth_read_only_directory",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth",\n "/my_other_path/eighth_read_only_directory",\n "Directory",\n true\n ],\n "_:0b3439f5-e916-4bb0-875b-01251ced359b": [\n "_:0b3439f5-e916-4bb0-875b-01251ced359b",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b": [\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh",\n "/GbFKKR/eleventh",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "/GbFKKR/twelfth",\n "File",\n true\n ],\n "_:b05fb645-e5b4-4261-ac08-84f2dbf2f4d6": [\n "baz",\n "/my_path/my_file_literal",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations.cwl_2] /private/tmp/docker_tmpcuw6t_2m$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpcuw6t_2m,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp53saqrze,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second,target=/GbFKKR/second_read_only_file,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmplrle3l4j/third,target=/my_path/third_writable_file \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth,target=/my_other_path/fourth_read_only_file,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth,target=/GbFKKR/sixth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpexcc8cx6/seventh,target=/my_path/seventh_writable_directory \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth,target=/my_other_path/eighth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmp07iolrgq/tenth_writable_directory_literal,target=/my_path/tenth_writable_directory_literal \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh,target=/GbFKKR/eleventh,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth,target=/GbFKKR/twelfth,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmphpy30rjt/my_file_literal,target=/my_path/my_file_literal,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp321qi8_g/20230605095036-465384.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n --env=LC_ALL=C \\\n docker.io/debian:stable-slim \\\n bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\necho "a" > first_writable_file\necho "b" > /my_path/third_writable_file\ntouch fifth_writable_directory/c\ntouch /my_path/seventh_writable_directory/d\nfind . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\n\' > /private/tmp/docker_tmpcuw6t_2m/log.txt\nINFO cwltool:job.py:905 [job iwdr_permutations.cwl_2] Max memory used: 0MiB\nERROR cwltool:job.py:395 Exception while running job\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 373, in _execute\n relink_initialworkdir(\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 103, in relink_initialworkdir\n shutil.rmtree(host_outdir_tgt)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 731, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 729, in rmtree\n os.rmdir(path)\nPermissionError: [Errno 13] Permission denied: \'/private/tmp/docker_tmpcuw6t_2m/sixth_read_only_directory\'\nWARNING cwltool:job.py:417 [job iwdr_permutations.cwl_2] completed permanentFail\nDEBUG cwltool:job.py:422 [job iwdr_permutations.cwl_2] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr_permutations.cwl_2] Removing input staging directory /private/tmp/docker_tmpy75vxspv\nDEBUG cwltool:job.py:454 [job iwdr_permutations.cwl_2] Removing temporary directory /private/tmp/docker_tmp53saqrze\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcuw6t_2m\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 2.665249376999782, 'start': 1685951434.82463, 'stop': 1685951437.489815, '$report_type': 'TestReport', 'item_index': 398, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_inplace', 'location': ('tests/test_iwdr.py', 188, 'test_iwdr_permutations_inplace'), 'keywords': {'test_iwdr_permutations_inplace': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl",\n "eighth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth"\n },\n "eleventh": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth"\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first"\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second"\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth"\n },\n "tenth": {\n "class": "Directory",\n "basename": "bar",\n "listing": []\n },\n "third": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr_permutations.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr_permutations.cwl_2] {\n "eighth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth",\n "basename": "eighth"\n },\n "eleventh": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh",\n "size": 0,\n "basename": "eleventh",\n "nameroot": "eleventh",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "size": 0,\n "basename": "twelfth",\n "nameroot": "twelfth",\n "nameext": ""\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "size": 0,\n "basename": "fourth",\n "nameroot": "fourth",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:0b3439f5-e916-4bb0-875b-01251ced359b"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "basename": "seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "basename": "sixth"\n },\n "tenth": {\n "class": "Directory",\n "basename": "bar",\n "listing": [],\n "location": "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b"\n },\n "third": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third",\n "size": 0,\n "basename": "third",\n "nameroot": "third",\n "nameext": ""\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr_permutations.cwl_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth",\n "/my_other_path/eighth_read_only_directory",\n "Directory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh",\n "/GbFKKR/eleventh",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "/GbFKKR/twelfth",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n false\n ],\n "_:0b3439f5-e916-4bb0-875b-01251ced359b": [\n "_:0b3439f5-e916-4bb0-875b-01251ced359b",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "/GbFKKR/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "/GbFKKR/sixth_read_only_directory",\n "Directory",\n false\n ],\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b": [\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third",\n "/my_path/third_writable_file",\n "WritableFile",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr_permutations.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\necho \\"a\\" > first_writable_file\\necho \\"b\\" > /my_path/third_writable_file\\ntouch fifth_writable_directory/c\\ntouch /my_path/seventh_writable_directory/d\\nfind . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\n"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr_permutations.cwl_2] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "/GbFKKR/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third",\n "/my_path/third_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "/GbFKKR/sixth_read_only_directory",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth",\n "/my_other_path/eighth_read_only_directory",\n "Directory",\n true\n ],\n "_:0b3439f5-e916-4bb0-875b-01251ced359b": [\n "_:0b3439f5-e916-4bb0-875b-01251ced359b",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b": [\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh",\n "/GbFKKR/eleventh",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "/GbFKKR/twelfth",\n "File",\n true\n ],\n "_:b05fb645-e5b4-4261-ac08-84f2dbf2f4d6": [\n "baz",\n "/my_path/my_file_literal",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations.cwl_2] /private/tmp/docker_tmpcuw6t_2m$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpcuw6t_2m,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp53saqrze,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second,target=/GbFKKR/second_read_only_file,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmplrle3l4j/third,target=/my_path/third_writable_file \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth,target=/my_other_path/fourth_read_only_file,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth,target=/GbFKKR/sixth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpexcc8cx6/seventh,target=/my_path/seventh_writable_directory \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth,target=/my_other_path/eighth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmp07iolrgq/tenth_writable_directory_literal,target=/my_path/tenth_writable_directory_literal \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh,target=/GbFKKR/eleventh,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth,target=/GbFKKR/twelfth,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmphpy30rjt/my_file_literal,target=/my_path/my_file_literal,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp321qi8_g/20230605095036-465384.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n --env=LC_ALL=C \\\n docker.io/debian:stable-slim \\\n bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\necho "a" > first_writable_file\necho "b" > /my_path/third_writable_file\ntouch fifth_writable_directory/c\ntouch /my_path/seventh_writable_directory/d\nfind . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\n\' > /private/tmp/docker_tmpcuw6t_2m/log.txt\nINFO cwltool:job.py:905 [job iwdr_permutations.cwl_2] Max memory used: 0MiB\nERROR cwltool:job.py:395 Exception while running job\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 373, in _execute\n relink_initialworkdir(\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 103, in relink_initialworkdir\n shutil.rmtree(host_outdir_tgt)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 731, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 729, in rmtree\n os.rmdir(path)\nPermissionError: [Errno 13] Permission denied: \'/private/tmp/docker_tmpcuw6t_2m/sixth_read_only_directory\'\nWARNING cwltool:job.py:417 [job iwdr_permutations.cwl_2] completed permanentFail\nDEBUG cwltool:job.py:422 [job iwdr_permutations.cwl_2] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr_permutations.cwl_2] Removing input staging directory /private/tmp/docker_tmpy75vxspv\nDEBUG cwltool:job.py:454 [job iwdr_permutations.cwl_2] Removing temporary directory /private/tmp/docker_tmp53saqrze\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcuw6t_2m\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.0014437290001296788, 'start': 1685951437.5007098, 'stop': 1685951437.502156, '$report_type': 'TestReport', 'item_index': 398, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_iwdr.py::test_iwdr_permutations_inplace + location: ('tests/test_iwdr.py', 188, 'test_iwdr_permutations_inplace') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_iwdr.py::test_iwdr_permutations_singularity + location: ('tests/test_iwdr.py', 249, 'test_iwdr_permutations_singularity') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_singularity', 'location': ('tests/test_iwdr.py', 249, 'test_iwdr_permutations_singularity'), 'keywords': {'test_iwdr_permutations_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 250, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000361376000000746, 'start': 1685951437.5041401, 'stop': 1685951437.504503, '$report_type': 'TestReport', 'item_index': 399, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_singularity', 'location': ('tests/test_iwdr.py', 249, 'test_iwdr_permutations_singularity'), 'keywords': {'test_iwdr_permutations_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00029616200026794104, 'start': 1685951437.505357, 'stop': 1685951437.505656, '$report_type': 'TestReport', 'item_index': 399, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_iwdr.py::test_iwdr_permutations_singularity + location: ('tests/test_iwdr.py', 249, 'test_iwdr_permutations_singularity') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_iwdr.py::test_iwdr_permutations_singularity_inplace + location: ('tests/test_iwdr.py', 313, 'test_iwdr_permutations_singularity_inplace') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_singularity_inplace', 'location': ('tests/test_iwdr.py', 313, 'test_iwdr_permutations_singularity_inplace'), 'keywords': {'test_iwdr_permutations_singularity_inplace': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 314, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005646749996230938, 'start': 1685951437.507093, 'stop': 1685951437.507661, '$report_type': 'TestReport', 'item_index': 400, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_singularity_inplace', 'location': ('tests/test_iwdr.py', 313, 'test_iwdr_permutations_singularity_inplace'), 'keywords': {'test_iwdr_permutations_singularity_inplace': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004171069995209109, 'start': 1685951437.508895, 'stop': 1685951437.509314, '$report_type': 'TestReport', 'item_index': 400, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_iwdr.py::test_iwdr_permutations_singularity_inplace + location: ('tests/test_iwdr.py', 313, 'test_iwdr_permutations_singularity_inplace') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_js_sandbox.py::test_node_version[v0.8.26\n-False] + location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.8.26\\n-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v0.8.26\\n-False]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.8.26\\n-False]'), 'keywords': {'test_node_version[v0.8.26\\n-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'v0.8.26\\n-False': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011338710000927676, 'start': 1685951437.510889, 'stop': 1685951437.512025, '$report_type': 'TestReport', 'item_index': 401, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v0.8.26\\n-False]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.8.26\\n-False]'), 'keywords': {'test_node_version[v0.8.26\\n-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'v0.8.26\\n-False': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0015750470001876238, 'start': 1685951437.5124109, 'stop': 1685951437.513988, '$report_type': 'TestReport', 'item_index': 401, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v0.8.26\\n-False]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.8.26\\n-False]'), 'keywords': {'test_node_version[v0.8.26\\n-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'v0.8.26\\n-False': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00038685999970766716, 'start': 1685951437.514486, 'stop': 1685951437.5148742, '$report_type': 'TestReport', 'item_index': 401, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_js_sandbox.py::test_node_version[v0.8.26\n-False] + location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.8.26\\n-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_js_sandbox.py::test_node_version[v0.10.25\n-False] + location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.10.25\\n-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v0.10.25\\n-False]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.10.25\\n-False]'), 'keywords': {'test_node_version[v0.10.25\\n-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'v0.10.25\\n-False': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006212739999682526, 'start': 1685951437.5158331, 'stop': 1685951437.516455, '$report_type': 'TestReport', 'item_index': 402, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v0.10.25\\n-False]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.10.25\\n-False]'), 'keywords': {'test_node_version[v0.10.25\\n-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'v0.10.25\\n-False': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0011852540001200396, 'start': 1685951437.516829, 'stop': 1685951437.518015, '$report_type': 'TestReport', 'item_index': 402, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v0.10.25\\n-False]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.10.25\\n-False]'), 'keywords': {'test_node_version[v0.10.25\\n-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'v0.10.25\\n-False': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00042883900005108444, 'start': 1685951437.518573, 'stop': 1685951437.519003, '$report_type': 'TestReport', 'item_index': 402, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_js_sandbox.py::test_node_version[v0.10.25\n-False] + location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.10.25\\n-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_js_sandbox.py::test_node_version[v0.10.26\n-True] + location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.10.26\\n-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v0.10.26\\n-True]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.10.26\\n-True]'), 'keywords': {'test_node_version[v0.10.26\\n-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'v0.10.26\\n-True': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011294169999018777, 'start': 1685951437.520193, 'stop': 1685951437.521324, '$report_type': 'TestReport', 'item_index': 403, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v0.10.26\\n-True]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.10.26\\n-True]'), 'keywords': {'test_node_version[v0.10.26\\n-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'v0.10.26\\n-True': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0015710719999333378, 'start': 1685951437.521848, 'stop': 1685951437.523422, '$report_type': 'TestReport', 'item_index': 403, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v0.10.26\\n-True]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.10.26\\n-True]'), 'keywords': {'test_node_version[v0.10.26\\n-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'v0.10.26\\n-True': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007154949998948723, 'start': 1685951437.5242581, 'stop': 1685951437.524976, '$report_type': 'TestReport', 'item_index': 403, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_js_sandbox.py::test_node_version[v0.10.26\n-True] + location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.10.26\\n-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_js_sandbox.py::test_node_version[v4.4.2\n-True] + location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v4.4.2\\n-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v4.4.2\\n-True]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v4.4.2\\n-True]'), 'keywords': {'test_node_version[v4.4.2\\n-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'v4.4.2\\n-True': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006095879998611053, 'start': 1685951437.526324, 'stop': 1685951437.526934, '$report_type': 'TestReport', 'item_index': 404, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v4.4.2\\n-True]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v4.4.2\\n-True]'), 'keywords': {'test_node_version[v4.4.2\\n-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'v4.4.2\\n-True': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0013060789997325628, 'start': 1685951437.5272808, 'stop': 1685951437.528588, '$report_type': 'TestReport', 'item_index': 404, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v4.4.2\\n-True]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v4.4.2\\n-True]'), 'keywords': {'test_node_version[v4.4.2\\n-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'v4.4.2\\n-True': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00032771899986983044, 'start': 1685951437.5289862, 'stop': 1685951437.529315, '$report_type': 'TestReport', 'item_index': 404, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_js_sandbox.py::test_node_version[v4.4.2\n-True] + location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v4.4.2\\n-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_js_sandbox.py::test_node_version[v7.7.3\n-True] + location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v7.7.3\\n-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v7.7.3\\n-True]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v7.7.3\\n-True]'), 'keywords': {'test_node_version[v7.7.3\\n-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'v7.7.3\\n-True': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008541689994672197, 'start': 1685951437.530613, 'stop': 1685951437.531469, '$report_type': 'TestReport', 'item_index': 405, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v7.7.3\\n-True]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v7.7.3\\n-True]'), 'keywords': {'test_node_version[v7.7.3\\n-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'v7.7.3\\n-True': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0011615169996730401, 'start': 1685951437.531994, 'stop': 1685951437.533157, '$report_type': 'TestReport', 'item_index': 405, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v7.7.3\\n-True]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v7.7.3\\n-True]'), 'keywords': {'test_node_version[v7.7.3\\n-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'v7.7.3\\n-True': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00045812500047759386, 'start': 1685951437.533797, 'stop': 1685951437.534257, '$report_type': 'TestReport', 'item_index': 405, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_js_sandbox.py::test_node_version[v7.7.3\n-True] + location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v7.7.3\\n-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions + location: ('tests/test_js_sandbox.py', 36, 'test_value_from_two_concatenated_expressions') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions', 'location': ('tests/test_js_sandbox.py', 36, 'test_value_from_two_concatenated_expressions'), 'keywords': {'test_value_from_two_concatenated_expressions': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002535580006224336, 'start': 1685951437.535306, 'stop': 1685951437.5355608, '$report_type': 'TestReport', 'item_index': 406, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method_no_iteration', 'location': ('tests/test_loop.py', 174, 'test_loop_with_all_output_method_no_iteration'), 'keywords': {'test_loop_with_all_output_method_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/all-output-loop-no-iteration.cwl:25:7: object id 'tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _7] start\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step subworkflow_2\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _7] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/all-output-loop-no-iteration.cwl:25:7: object id \'tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step subworkflow_2\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_2] loop condition $(inputs.i1 < 1) evaluated to False at iteration 0\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_2] inputs was {\n "i1": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/o1": []\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _7] outputs {\n "o1": []\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa1ulhxe7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9535392379993937, 'start': 1685951436.7428648, 'stop': 1685951437.696382, '$report_type': 'TestReport', 'item_index': 433, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method_no_iteration', 'location': ('tests/test_loop.py', 174, 'test_loop_with_all_output_method_no_iteration'), 'keywords': {'test_loop_with_all_output_method_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/all-output-loop-no-iteration.cwl:25:7: object id 'tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _7] start\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step subworkflow_2\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _7] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/all-output-loop-no-iteration.cwl:25:7: object id \'tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step subworkflow_2\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_2] loop condition $(inputs.i1 < 1) evaluated to False at iteration 0\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_2] inputs was {\n "i1": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/o1": []\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _7] outputs {\n "o1": []\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa1ulhxe7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00035875300000043353, 'start': 1685951437.6971169, 'stop': 1685951437.6974778, '$report_type': 'TestReport', 'item_index': 433, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_loop_with_all_output_method_no_iteration + location: ('tests/test_loop.py', 174, 'test_loop_with_all_output_method_no_iteration') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_value_from', 'location': ('tests/test_loop.py', 187, 'test_loop_value_from'), 'keywords': {'test_loop_value_from': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002861479997591232, 'start': 1685951437.698797, 'stop': 1685951437.699084, '$report_type': 'TestReport', 'item_index': 434, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_loop_value_from + location: ('tests/test_loop.py', 187, 'test_loop_value_from') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_warn_large_inputs', 'location': ('tests/test_ext.py', 264, 'test_warn_large_inputs'), 'keywords': {'test_warn_large_inputs': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', '/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\'\nWARNING cwltool:process.py:795 tests/wf/listing_v1_0.cwl:5:3: Recursive directory listing has resulted in a large number of File\n objects (5) passed to the input parameter \'d\'. This may negatively\n affect workflow performance and memory use.\n \n If this is a problem, use the hint \'cwltool:LoadListingRequirement\'\n with "shallow_listing" or "no_listing" to change the directory\n listing behavior:\n \n $namespaces:\n cwltool: "http://commonwl.org/cwltool#"\n hints:\n cwltool:LoadListingRequirement:\n loadListing: shallow_listing\n \nDEBUG cwltool:command_line_tool.py:982 [job listing_v1_0.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\nDEBUG cwltool:command_line_tool.py:988 [job listing_v1_0.cwl] {\n "d": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4",\n "basename": "tmp4",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha",\n "basename": "alpha",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta",\n "basename": "delta",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot",\n "basename": "foxtrot",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo",\n "basename": "echo",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker",\n "basename": "baker",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie",\n "basename": "charlie",\n "size": 0\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job listing_v1_0.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/foxtrot",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/echo",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/baker",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/charlie",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job listing_v1_0.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.d.listing[0].listing[0])"\n }\n]\nDEBUG cwltool:job.py:215 [job listing_v1_0.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job listing_v1_0.cwl] /private/tmp/docker_tmp546a07j8$ echo \\\n /private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job listing_v1_0.cwl] completed success\nDEBUG cwltool:job.py:422 [job listing_v1_0.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job listing_v1_0.cwl] Removing input staging directory /private/tmp/docker_tmpcpbuwmdl\nDEBUG cwltool:job.py:454 [job listing_v1_0.cwl] Removing temporary directory /private/tmp/docker_tmp24i8q5y1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp546a07j8\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.734424934999879, 'start': 1685951436.99087, 'stop': 1685951437.72528, '$report_type': 'TestReport', 'item_index': 379, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_warn_large_inputs', 'location': ('tests/test_ext.py', 264, 'test_warn_large_inputs'), 'keywords': {'test_warn_large_inputs': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', '/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\'\nWARNING cwltool:process.py:795 tests/wf/listing_v1_0.cwl:5:3: Recursive directory listing has resulted in a large number of File\n objects (5) passed to the input parameter \'d\'. This may negatively\n affect workflow performance and memory use.\n \n If this is a problem, use the hint \'cwltool:LoadListingRequirement\'\n with "shallow_listing" or "no_listing" to change the directory\n listing behavior:\n \n $namespaces:\n cwltool: "http://commonwl.org/cwltool#"\n hints:\n cwltool:LoadListingRequirement:\n loadListing: shallow_listing\n \nDEBUG cwltool:command_line_tool.py:982 [job listing_v1_0.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\nDEBUG cwltool:command_line_tool.py:988 [job listing_v1_0.cwl] {\n "d": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4",\n "basename": "tmp4",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha",\n "basename": "alpha",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta",\n "basename": "delta",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot",\n "basename": "foxtrot",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo",\n "basename": "echo",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker",\n "basename": "baker",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie",\n "basename": "charlie",\n "size": 0\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job listing_v1_0.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/foxtrot",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/echo",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/baker",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/charlie",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job listing_v1_0.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.d.listing[0].listing[0])"\n }\n]\nDEBUG cwltool:job.py:215 [job listing_v1_0.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job listing_v1_0.cwl] /private/tmp/docker_tmp546a07j8$ echo \\\n /private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job listing_v1_0.cwl] completed success\nDEBUG cwltool:job.py:422 [job listing_v1_0.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job listing_v1_0.cwl] Removing input staging directory /private/tmp/docker_tmpcpbuwmdl\nDEBUG cwltool:job.py:454 [job listing_v1_0.cwl] Removing temporary directory /private/tmp/docker_tmp24i8q5y1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp546a07j8\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0004214670007058885, 'start': 1685951437.726537, 'stop': 1685951437.726959, '$report_type': 'TestReport', 'item_index': 379, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_warn_large_inputs + location: ('tests/test_ext.py', 264, 'test_warn_large_inputs') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_fetch.py::test_fetcher + location: ('tests/test_fetch.py', 52, 'test_fetcher') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_fetcher', 'location': ('tests/test_fetch.py', 52, 'test_fetcher'), 'keywords': {'test_fetcher': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002361979995839647, 'start': 1685951437.728332, 'stop': 1685951437.728569, '$report_type': 'TestReport', 'item_index': 380, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_no_ext', 'location': ('tests/test_loop.py', 20, 'test_validate_loop_fail_no_ext'), 'keywords': {'test_validate_loop_fail_no_ext': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/single-var-loop.cwl:15:1: checking field 'steps'\ntests/loop/single-var-loop.cwl:16:3: checking object 'tests/loop/single-var-loop.cwl#subworkflow'\ntests/loop/single-var-loop.cwl:28:5: checking field 'requirements'\ntests/loop/single-var-loop.cwl:29:7: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#Loop'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/single-var-loop.cwl:15:1: checking field 'steps'\ntests/loop/single-var-loop.cwl:16:3: checking object 'tests/loop/single-var-loop.cwl#subworkflow'\ntests/loop/single-var-loop.cwl:28:5: checking field 'requirements'\ntests/loop/single-var-loop.cwl:29:7: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#Loop'")], 'duration': 0.9462879800003066, 'start': 1685951436.9938939, 'stop': 1685951437.94016, '$report_type': 'TestReport', 'item_index': 419, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_no_ext', 'location': ('tests/test_loop.py', 20, 'test_validate_loop_fail_no_ext'), 'keywords': {'test_validate_loop_fail_no_ext': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/single-var-loop.cwl:15:1: checking field 'steps'\ntests/loop/single-var-loop.cwl:16:3: checking object 'tests/loop/single-var-loop.cwl#subworkflow'\ntests/loop/single-var-loop.cwl:28:5: checking field 'requirements'\ntests/loop/single-var-loop.cwl:29:7: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#Loop'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/single-var-loop.cwl:15:1: checking field 'steps'\ntests/loop/single-var-loop.cwl:16:3: checking object 'tests/loop/single-var-loop.cwl#subworkflow'\ntests/loop/single-var-loop.cwl:28:5: checking field 'requirements'\ntests/loop/single-var-loop.cwl:29:7: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#Loop'")], 'duration': 0.0003070539996770094, 'start': 1685951437.94085, 'stop': 1685951437.941161, '$report_type': 'TestReport', 'item_index': 419, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_no_ext + location: ('tests/test_loop.py', 20, 'test_validate_loop_fail_no_ext') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_scatter + location: ('tests/test_loop.py', 29, 'test_validate_loop_fail_scatter') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_scatter', 'location': ('tests/test_loop.py', 29, 'test_validate_loop_fail_scatter'), 'keywords': {'test_validate_loop_fail_scatter': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004007010002169409, 'start': 1685951437.9424949, 'stop': 1685951437.9428968, '$report_type': 'TestReport', 'item_index': 420, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions', 'location': ('tests/test_js_sandbox.py', 36, 'test_value_from_two_concatenated_expressions'), 'keywords': {'test_value_from_two_concatenated_expressions': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\'\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "valueFrom": "$(\\"a \\")$(\\"string\\")",\n "position": [\n 0,\n "file1"\n ],\n "datum": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "dirname": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066"\n }\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mINFO\x1b[0m [job vf-concat.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c$ echo \\\n \'a string\' > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c/output.txt\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mINFO\x1b[0m [job vf-concat.cwl] completed success\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] outputs {\n "out": "a string\\n"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/epq_ftst\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job vf-concat.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\nDEBUG cwltool:command_line_tool.py:988 [job vf-concat.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job vf-concat.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job vf-concat.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "valueFrom": "$(\\"a \\")$(\\"string\\")",\n "position": [\n 0,\n "file1"\n ],\n "datum": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "dirname": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job vf-concat.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job vf-concat.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c$ echo \\\n \'a string\' > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job vf-concat.cwl] completed success\nDEBUG cwltool:job.py:422 [job vf-concat.cwl] outputs {\n "out": "a string\\n"\n}\nDEBUG cwltool:job.py:446 [job vf-concat.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es\nDEBUG cwltool:job.py:454 [job vf-concat.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/epq_ftst\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c')], 'duration': 0.5434311580002031, 'start': 1685951437.53597, 'stop': 1685951438.07939, '$report_type': 'TestReport', 'item_index': 406, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions', 'location': ('tests/test_js_sandbox.py', 36, 'test_value_from_two_concatenated_expressions'), 'keywords': {'test_value_from_two_concatenated_expressions': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\'\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "valueFrom": "$(\\"a \\")$(\\"string\\")",\n "position": [\n 0,\n "file1"\n ],\n "datum": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "dirname": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066"\n }\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mINFO\x1b[0m [job vf-concat.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c$ echo \\\n \'a string\' > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c/output.txt\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mINFO\x1b[0m [job vf-concat.cwl] completed success\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] outputs {\n "out": "a string\\n"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/epq_ftst\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job vf-concat.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\nDEBUG cwltool:command_line_tool.py:988 [job vf-concat.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job vf-concat.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job vf-concat.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "valueFrom": "$(\\"a \\")$(\\"string\\")",\n "position": [\n 0,\n "file1"\n ],\n "datum": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "dirname": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job vf-concat.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job vf-concat.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c$ echo \\\n \'a string\' > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job vf-concat.cwl] completed success\nDEBUG cwltool:job.py:422 [job vf-concat.cwl] outputs {\n "out": "a string\\n"\n}\nDEBUG cwltool:job.py:446 [job vf-concat.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es\nDEBUG cwltool:job.py:454 [job vf-concat.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/epq_ftst\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c')], 'duration': 0.0004654399999708403, 'start': 1685951438.0806642, 'stop': 1685951438.081131, '$report_type': 'TestReport', 'item_index': 406, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions + location: ('tests/test_js_sandbox.py', 36, 'test_value_from_two_concatenated_expressions') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_podman + location: ('tests/test_js_sandbox.py', 72, 'test_value_from_two_concatenated_expressions_podman') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_podman', 'location': ('tests/test_js_sandbox.py', 72, 'test_value_from_two_concatenated_expressions_podman'), 'keywords': {'test_value_from_two_concatenated_expressions_podman': 1, 'skipif': 1, 'pytestmark': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_js_sandbox.py', 73, 'Skipped: Requires the podman executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00030104899997240864, 'start': 1685951438.08305, 'stop': 1685951438.083353, '$report_type': 'TestReport', 'item_index': 407, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_podman', 'location': ('tests/test_js_sandbox.py', 72, 'test_value_from_two_concatenated_expressions_podman'), 'keywords': {'test_value_from_two_concatenated_expressions_podman': 1, 'skipif': 1, 'pytestmark': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00024386600034631556, 'start': 1685951438.084286, 'stop': 1685951438.0845308, '$report_type': 'TestReport', 'item_index': 407, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_podman + location: ('tests/test_js_sandbox.py', 72, 'test_value_from_two_concatenated_expressions_podman') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_singularity + location: ('tests/test_js_sandbox.py', 92, 'test_value_from_two_concatenated_expressions_singularity') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_singularity', 'location': ('tests/test_js_sandbox.py', 92, 'test_value_from_two_concatenated_expressions_singularity'), 'keywords': {'test_value_from_two_concatenated_expressions_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_js_sandbox.py', 93, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00024004999977478292, 'start': 1685951438.08574, 'stop': 1685951438.085981, '$report_type': 'TestReport', 'item_index': 408, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_singularity', 'location': ('tests/test_js_sandbox.py', 92, 'test_value_from_two_concatenated_expressions_singularity'), 'keywords': {'test_value_from_two_concatenated_expressions_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00024955099979706574, 'start': 1685951438.0868962, 'stop': 1685951438.087147, '$report_type': 'TestReport', 'item_index': 408, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_singularity + location: ('tests/test_js_sandbox.py', 92, 'test_value_from_two_concatenated_expressions_singularity') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_multi_source_loop_input_fail_no_requirement + location: ('tests/test_loop.py', 262, 'test_multi_source_loop_input_fail_no_requirement') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input_fail_no_requirement', 'location': ('tests/test_loop.py', 262, 'test_multi_source_loop_input_fail_no_requirement'), 'keywords': {'test_multi_source_loop_input_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00029997300043760333, 'start': 1685951438.0884101, 'stop': 1685951438.088712, '$report_type': 'TestReport', 'item_index': 440, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_fetcher', 'location': ('tests/test_fetch.py', 52, 'test_fetcher'), 'keywords': {'test_fetcher': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "baseCommand": "echo",\n "class": "CommandLineTool",\n "cwlVersion": "v1.0",\n "id": "baz:bar/foo.cwl#bar/foo.cwl",\n "inputs": [],\n "outputs": []\n}'), ('Captured stderr call', "\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?")], 'duration': 0.715932681000595, 'start': 1685951437.7290199, 'stop': 1685951438.444936, '$report_type': 'TestReport', 'item_index': 380, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_fetcher', 'location': ('tests/test_fetch.py', 52, 'test_fetcher'), 'keywords': {'test_fetcher': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "baseCommand": "echo",\n "class": "CommandLineTool",\n "cwlVersion": "v1.0",\n "id": "baz:bar/foo.cwl#bar/foo.cwl",\n "inputs": [],\n "outputs": []\n}'), ('Captured stderr call', "\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?")], 'duration': 0.0003046749998247833, 'start': 1685951438.445558, 'stop': 1685951438.445864, '$report_type': 'TestReport', 'item_index': 380, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_fetch.py::test_fetcher + location: ('tests/test_fetch.py', 52, 'test_fetcher') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_fetch.py::test_resolve_local[tests/echo.cwl-/tests/echo.cwl] + location: ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006597010005862103, 'start': 1685951438.4470139, 'stop': 1685951438.447675, '$report_type': 'TestReport', 'item_index': 381, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006710289999318775, 'start': 1685951438.448179, 'stop': 1685951438.448852, '$report_type': 'TestReport', 'item_index': 381, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00039458500032196753, 'start': 1685951438.449436, 'stop': 1685951438.449832, '$report_type': 'TestReport', 'item_index': 381, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_fetch.py::test_resolve_local[tests/echo.cwl-/tests/echo.cwl] + location: ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_fetch.py::test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main] + location: ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006498700004158309, 'start': 1685951438.4510012, 'stop': 1685951438.451652, '$report_type': 'TestReport', 'item_index': 382, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005966490007267566, 'start': 1685951438.452197, 'stop': 1685951438.4527948, '$report_type': 'TestReport', 'item_index': 382, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00036924100004398497, 'start': 1685951438.453301, 'stop': 1685951438.453671, '$report_type': 'TestReport', 'item_index': 382, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_fetch.py::test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main] + location: ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl] + location: ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005771220003225608, 'start': 1685951438.4548259, 'stop': 1685951438.455405, '$report_type': 'TestReport', 'item_index': 383, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006573210002898122, 'start': 1685951438.4559438, 'stop': 1685951438.456602, '$report_type': 'TestReport', 'item_index': 383, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005036920001657563, 'start': 1685951438.457206, 'stop': 1685951438.4577112, '$report_type': 'TestReport', 'item_index': 383, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl] + location: ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main] + location: ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007643929993719212, 'start': 1685951438.459253, 'stop': 1685951438.4600189, '$report_type': 'TestReport', 'item_index': 384, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006920289997651707, 'start': 1685951438.460586, 'stop': 1685951438.46128, '$report_type': 'TestReport', 'item_index': 384, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00026139400051761186, 'start': 1685951438.461681, 'stop': 1685951438.461944, '$report_type': 'TestReport', 'item_index': 384, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main] + location: ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_http_input.py::test_http_path_mapping + location: ('tests/test_http_input.py', 13, 'test_http_path_mapping') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_http_input.py::test_http_path_mapping', 'location': ('tests/test_http_input.py', 13, 'test_http_path_mapping'), 'keywords': {'test_http_path_mapping': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014472699995167204, 'start': 1685951438.462792, 'stop': 1685951438.46424, '$report_type': 'TestReport', 'item_index': 385, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_http_input.py::test_http_path_mapping', 'location': ('tests/test_http_input.py', 13, 'test_http_path_mapping'), 'keywords': {'test_http_path_mapping': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.003667699999823526, 'start': 1685951438.464559, 'stop': 1685951438.468228, '$report_type': 'TestReport', 'item_index': 385, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_http_input.py::test_http_path_mapping', 'location': ('tests/test_http_input.py', 13, 'test_http_path_mapping'), 'keywords': {'test_http_path_mapping': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00032206000014411984, 'start': 1685951438.468769, 'stop': 1685951438.469093, '$report_type': 'TestReport', 'item_index': 385, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_http_input.py::test_http_path_mapping + location: ('tests/test_http_input.py', 13, 'test_http_path_mapping') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_http_input.py::test_modification_date + location: ('tests/test_http_input.py', 36, 'test_modification_date') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_http_input.py::test_modification_date', 'location': ('tests/test_http_input.py', 36, 'test_modification_date'), 'keywords': {'test_modification_date': 1, 'skipif': 1, 'pytestmark': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008432869999523973, 'start': 1685951438.47001, 'stop': 1685951438.4708538, '$report_type': 'TestReport', 'item_index': 386, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--debug]'), 'keywords': {'test_cache_relative_paths[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_5] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_5] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_5] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_5] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmp47n97al1/stgb620e7cc-3aa3-4431-ae41-b9e220a3c7c3/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmp47n97al1/stgb620e7cc-3aa3-4431-ae41-b9e220a3c7c3/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job secondary-files.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_5] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_5] Removing input staging directory /private/tmp/docker_tmp47n97al1\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_5] Removing temporary directory /private/tmp/docker_tmpkmqmkc1i\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cacheqsaiiuf2\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_6] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_6] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cachekzcrurqy\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.7288621939997029, 'start': 1685951436.8263628, 'stop': 1685951438.5551841, '$report_type': 'TestReport', 'item_index': 302, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--debug]'), 'keywords': {'test_cache_relative_paths[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_5] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_5] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_5] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_5] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmp47n97al1/stgb620e7cc-3aa3-4431-ae41-b9e220a3c7c3/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmp47n97al1/stgb620e7cc-3aa3-4431-ae41-b9e220a3c7c3/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job secondary-files.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_5] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_5] Removing input staging directory /private/tmp/docker_tmp47n97al1\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_5] Removing temporary directory /private/tmp/docker_tmpkmqmkc1i\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cacheqsaiiuf2\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_6] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_6] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cachekzcrurqy\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005429989996628137, 'start': 1685951438.555991, 'stop': 1685951438.556535, '$report_type': 'TestReport', 'item_index': 302, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cache_relative_paths[--debug] + location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--debug]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cache_relative_paths[--parallel --debug] + location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel --debug]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel --debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel --debug]'), 'keywords': {'test_cache_relative_paths[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016512539996256237, 'start': 1685951438.558201, 'stop': 1685951438.559854, '$report_type': 'TestReport', 'item_index': 303, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_double_overwrite', 'location': ('tests/test_ext.py', 76, 'test_double_overwrite'), 'keywords': {'test_double_overwrite': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m [workflow ] start\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/python:3-slim']\n3-slim: Pulling from library/python\nDigest: sha256:eaee5f73efa9ae962d2077756292bc4878c04fcbc13dc168bb00cc365f35647e\nStatus: Image is up to date for python:3-slim\ndocker.io/library/python:3-slim\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmp_30_j4_2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_30_j4_2,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpb8gbxko8,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkj57te9v/20230605095036-573055.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step1] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step step2\n\x1b[1;30mINFO\x1b[0m [step step2] start\n\x1b[1;30mINFO\x1b[0m [job step2] /private/tmp/docker_tmp9iy54f2l$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp9iy54f2l,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqpnyw3w,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphp0i1stc/20230605095037-615502.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step2] completed success\n\x1b[1;30mINFO\x1b[0m [step step2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow ] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl",\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value"\n }\n}\nDEBUG cwltool:workflow_job.py:498 [workflow ] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\nINFO cwltool:workflow_job.py:765 [workflow ] start\nDEBUG cwltool:workflow_job.py:777 [workflow ] inputs {\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow ] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/python:3-slim\']\nDEBUG cwltool:job.py:215 [job step1] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp_30_j4_2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_30_j4_2,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpb8gbxko8,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkj57te9v/20230605095036-573055.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpm2j47r1m\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpb8gbxko8\nINFO cwltool:workflow_job.py:613 [workflow ] starting step step2\nDEBUG cwltool:workflow_job.py:727 [step step2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2] start\nDEBUG cwltool:command_line_tool.py:982 [job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step2\nDEBUG cwltool:command_line_tool.py:988 [job step2] {\n "r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step2] path mappings is {\n "file:///private/tmp/docker_tmp_30_j4_2/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job step2] initial work dir {\n "file:///private/tmp/docker_tmp_30_j4_2/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step2] /private/tmp/docker_tmp9iy54f2l$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp9iy54f2l,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqpnyw3w,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphp0i1stc/20230605095037-615502.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step2] completed success\nDEBUG cwltool:job.py:422 [job step2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2] completed success\nINFO cwltool:workflow_job.py:539 [workflow ] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow ] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step2] Removing input staging directory /private/tmp/docker_tmpe8awqq_l\nDEBUG cwltool:job.py:454 [job step2] Removing temporary directory /private/tmp/docker_tmpdqpnyw3w\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_30_j4_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9iy54f2l\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpflv_h189\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 5.5616510429999835, 'start': 1685951433.0829089, 'stop': 1685951438.644423, '$report_type': 'TestReport', 'item_index': 369, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_double_overwrite', 'location': ('tests/test_ext.py', 76, 'test_double_overwrite'), 'keywords': {'test_double_overwrite': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m [workflow ] start\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/python:3-slim']\n3-slim: Pulling from library/python\nDigest: sha256:eaee5f73efa9ae962d2077756292bc4878c04fcbc13dc168bb00cc365f35647e\nStatus: Image is up to date for python:3-slim\ndocker.io/library/python:3-slim\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmp_30_j4_2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_30_j4_2,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpb8gbxko8,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkj57te9v/20230605095036-573055.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step1] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step step2\n\x1b[1;30mINFO\x1b[0m [step step2] start\n\x1b[1;30mINFO\x1b[0m [job step2] /private/tmp/docker_tmp9iy54f2l$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp9iy54f2l,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqpnyw3w,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphp0i1stc/20230605095037-615502.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step2] completed success\n\x1b[1;30mINFO\x1b[0m [step step2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow ] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl",\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value"\n }\n}\nDEBUG cwltool:workflow_job.py:498 [workflow ] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\nINFO cwltool:workflow_job.py:765 [workflow ] start\nDEBUG cwltool:workflow_job.py:777 [workflow ] inputs {\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow ] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/python:3-slim\']\nDEBUG cwltool:job.py:215 [job step1] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp_30_j4_2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_30_j4_2,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpb8gbxko8,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkj57te9v/20230605095036-573055.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpm2j47r1m\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpb8gbxko8\nINFO cwltool:workflow_job.py:613 [workflow ] starting step step2\nDEBUG cwltool:workflow_job.py:727 [step step2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2] start\nDEBUG cwltool:command_line_tool.py:982 [job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step2\nDEBUG cwltool:command_line_tool.py:988 [job step2] {\n "r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step2] path mappings is {\n "file:///private/tmp/docker_tmp_30_j4_2/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job step2] initial work dir {\n "file:///private/tmp/docker_tmp_30_j4_2/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step2] /private/tmp/docker_tmp9iy54f2l$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp9iy54f2l,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqpnyw3w,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphp0i1stc/20230605095037-615502.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step2] completed success\nDEBUG cwltool:job.py:422 [job step2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2] completed success\nINFO cwltool:workflow_job.py:539 [workflow ] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow ] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step2] Removing input staging directory /private/tmp/docker_tmpe8awqq_l\nDEBUG cwltool:job.py:454 [job step2] Removing temporary directory /private/tmp/docker_tmpdqpnyw3w\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_30_j4_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9iy54f2l\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpflv_h189\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005781970003226888, 'start': 1685951438.645545, 'stop': 1685951438.646125, '$report_type': 'TestReport', 'item_index': 369, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_double_overwrite + location: ('tests/test_ext.py', 76, 'test_double_overwrite') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_ext.py::test_disable_file_overwrite_without_ext + location: ('tests/test_ext.py', 106, 'test_disable_file_overwrite_without_ext') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_file_overwrite_without_ext', 'location': ('tests/test_ext.py', 106, 'test_disable_file_overwrite_without_ext'), 'keywords': {'test_disable_file_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018297330007044366, 'start': 1685951438.64766, 'stop': 1685951438.649492, '$report_type': 'TestReport', 'item_index': 370, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_value_from', 'location': ('tests/test_loop.py', 187, 'test_loop_value_from'), 'keywords': {'test_loop_value_from': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/value-from-loop.cwl:28:7: object id 'tests/loop/value-from-loop.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _8] start\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step subworkflow_3\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _8] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/value-from-loop.cwl:28:7: object id \'tests/loop/value-from-loop.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _8] start\nDEBUG cwltool:workflow_job.py:777 [workflow _8] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step subworkflow_3\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_3] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_3] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _8] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaelm08fz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.057735744000638, 'start': 1685951437.699521, 'stop': 1685951438.7572322, '$report_type': 'TestReport', 'item_index': 434, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_value_from', 'location': ('tests/test_loop.py', 187, 'test_loop_value_from'), 'keywords': {'test_loop_value_from': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/value-from-loop.cwl:28:7: object id 'tests/loop/value-from-loop.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _8] start\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step subworkflow_3\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _8] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/value-from-loop.cwl:28:7: object id \'tests/loop/value-from-loop.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _8] start\nDEBUG cwltool:workflow_job.py:777 [workflow _8] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step subworkflow_3\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_3] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_3] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _8] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaelm08fz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00037351199989643646, 'start': 1685951438.758164, 'stop': 1685951438.758539, '$report_type': 'TestReport', 'item_index': 434, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_loop_value_from + location: ('tests/test_loop.py', 187, 'test_loop_value_from') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_loop_value_from_fail_no_requirement + location: ('tests/test_loop.py', 200, 'test_loop_value_from_fail_no_requirement') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_value_from_fail_no_requirement', 'location': ('tests/test_loop.py', 200, 'test_loop_value_from_fail_no_requirement'), 'keywords': {'test_loop_value_from_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003256449999753386, 'start': 1685951438.760072, 'stop': 1685951438.760399, '$report_type': 'TestReport', 'item_index': 435, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_scatter', 'location': ('tests/test_loop.py', 29, 'test_validate_loop_fail_scatter'), 'keywords': {'test_validate_loop_fail_scatter': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-scatter.cwl:32:11: object id 'tests/loop/invalid-loop-scatter.cwl#subworkflow/i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-scatter.cwl:18:3: The `cwltool:Loop` clause is not compatible with the\n `scatter` directive.\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-scatter.cwl:32:11: object id 'tests/loop/invalid-loop-scatter.cwl#subworkflow/i1' previously defined\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-scatter.cwl:18:3: The `cwltool:Loop` clause is not compatible with the\n `scatter` directive.")], 'duration': 0.9162313860006179, 'start': 1685951437.943309, 'stop': 1685951438.859519, '$report_type': 'TestReport', 'item_index': 420, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_scatter', 'location': ('tests/test_loop.py', 29, 'test_validate_loop_fail_scatter'), 'keywords': {'test_validate_loop_fail_scatter': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-scatter.cwl:32:11: object id 'tests/loop/invalid-loop-scatter.cwl#subworkflow/i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-scatter.cwl:18:3: The `cwltool:Loop` clause is not compatible with the\n `scatter` directive.\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-scatter.cwl:32:11: object id 'tests/loop/invalid-loop-scatter.cwl#subworkflow/i1' previously defined\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-scatter.cwl:18:3: The `cwltool:Loop` clause is not compatible with the\n `scatter` directive.")], 'duration': 0.0002120910003213794, 'start': 1685951438.860019, 'stop': 1685951438.8602319, '$report_type': 'TestReport', 'item_index': 420, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_when', 'location': ('tests/test_loop.py', 39, 'test_validate_loop_fail_when'), 'keywords': {'test_validate_loop_fail_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0001864279993242235, 'start': 1685951438.861054, 'stop': 1685951438.861241, '$report_type': 'TestReport', 'item_index': 421, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_when + location: ('tests/test_loop.py', 39, 'test_validate_loop_fail_when') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_http_input.py::test_modification_date', 'location': ('tests/test_http_input.py', 36, 'test_modification_date'), 'keywords': {'test_modification_date': 1, 'skipif': 1, 'pytestmark': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO werkzeug:_internal.py:186 127.0.0.1 - - [05/Jun/2023 09:50:38] "GET /testfile.txt HTTP/1.1" 200 -')], 'duration': 0.5317395809997834, 'start': 1685951438.47117, 'stop': 1685951439.002898, '$report_type': 'TestReport', 'item_index': 386, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_http_input.py::test_modification_date', 'location': ('tests/test_http_input.py', 36, 'test_modification_date'), 'keywords': {'test_modification_date': 1, 'skipif': 1, 'pytestmark': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO werkzeug:_internal.py:186 127.0.0.1 - - [05/Jun/2023 09:50:38] "GET /testfile.txt HTTP/1.1" 200 -')], 'duration': 0.00039448400002584094, 'start': 1685951439.003603, 'stop': 1685951439.003999, '$report_type': 'TestReport', 'item_index': 386, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_http_input.py::test_modification_date + location: ('tests/test_http_input.py', 36, 'test_modification_date') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_input_deps.py::test_input_deps + location: ('tests/test_input_deps.py', 13, 'test_input_deps') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps', 'location': ('tests/test_input_deps.py', 13, 'test_input_deps'), 'keywords': {'test_input_deps': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002890409996325616, 'start': 1685951439.005383, 'stop': 1685951439.005673, '$report_type': 'TestReport', 'item_index': 387, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] +\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cacheyc1ic0v7\nINFO cwltool:main.py:13 pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input_fail_no_requirement', 'location': ('tests/test_loop.py', 262, 'test_multi_source_loop_input_fail_no_requirement'), 'keywords': {'test_multi_source_loop_input_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:59:7: object id \'tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:11: Source \'osmall\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:19: Source \'obig\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow ] start\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step loop\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step small_values\n\x1b[1;30mINFO\x1b[0m [step small_values] start\n\x1b[1;30mINFO\x1b[0m [step small_values] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step big_values\n\x1b[1;30mINFO\x1b[0m [step big_values] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 1 completed success\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step big_values] Cannot make job: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[step loop] completed permanentFail\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[workflow ] Cannot collect workflow output: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow ] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-multi-source-loop-no-requirement.cwl:59:7: object id \'tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:11: Source \'osmall\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:19: Source \'obig\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow ] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\nINFO cwltool:workflow_job.py:765 [workflow ] start\nDEBUG cwltool:workflow_job.py:777 [workflow ] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow ] starting step loop\nDEBUG cwltool:workflow_job.py:727 [step loop] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop] initialized from _:190467e8-291e-47f2-bb03-2b35d4dd8bb1\nINFO cwltool:workflow_job.py:765 [workflow loop] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step small_values\nDEBUG cwltool:workflow_job.py:727 [step small_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step small_values] start\nDEBUG cwltool:workflow_job.py:564 [step small_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step small_values] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step big_values\nDEBUG cwltool:workflow_job.py:727 [step big_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop] outputs {\n "obig": null,\n "osmall": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/osmall": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 1 completed success\nERROR cwltool:workflow_job.py:833 [step big_values] Cannot make job: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 745, in try_make_job\n callback({k["id"]: None for k in outputparms}, "skipped")\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 582, in receive_output\n self.do_output_callback(final_output_callback)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 545, in do_output_callback\n final_output_callback(wo, self.processStatus)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 429, in receive_output\n output_callback(output, processStatus)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 1020, in loop_callback\n object_from_state(\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 391, in object_from_state\n raise WorkflowException(\ncwltool.errors.WorkflowException: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nDEBUG cwltool:workflow_job.py:564 [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/osmall": [\n 2\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/obig": [\n null\n ]\n}\nWARNING cwltool:workflow_job.py:570 [step loop] completed permanentFail\nERROR cwltool:workflow_job.py:520 [workflow ] Cannot collect workflow output: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nINFO cwltool:workflow_job.py:539 [workflow ] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow ] outputs null\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7mewqrkl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp45f8r8g2\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 1.0215164639994327, 'start': 1685951438.089225, 'stop': 1685951439.110718, '$report_type': 'TestReport', 'item_index': 440, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input_fail_no_requirement', 'location': ('tests/test_loop.py', 262, 'test_multi_source_loop_input_fail_no_requirement'), 'keywords': {'test_multi_source_loop_input_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:59:7: object id \'tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:11: Source \'osmall\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:19: Source \'obig\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow ] start\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step loop\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step small_values\n\x1b[1;30mINFO\x1b[0m [step small_values] start\n\x1b[1;30mINFO\x1b[0m [step small_values] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step big_values\n\x1b[1;30mINFO\x1b[0m [step big_values] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 1 completed success\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step big_values] Cannot make job: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[step loop] completed permanentFail\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[workflow ] Cannot collect workflow output: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow ] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-multi-source-loop-no-requirement.cwl:59:7: object id \'tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:11: Source \'osmall\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:19: Source \'obig\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow ] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\nINFO cwltool:workflow_job.py:765 [workflow ] start\nDEBUG cwltool:workflow_job.py:777 [workflow ] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow ] starting step loop\nDEBUG cwltool:workflow_job.py:727 [step loop] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop] initialized from _:190467e8-291e-47f2-bb03-2b35d4dd8bb1\nINFO cwltool:workflow_job.py:765 [workflow loop] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step small_values\nDEBUG cwltool:workflow_job.py:727 [step small_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step small_values] start\nDEBUG cwltool:workflow_job.py:564 [step small_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step small_values] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step big_values\nDEBUG cwltool:workflow_job.py:727 [step big_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop] outputs {\n "obig": null,\n "osmall": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/osmall": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 1 completed success\nERROR cwltool:workflow_job.py:833 [step big_values] Cannot make job: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 745, in try_make_job\n callback({k["id"]: None for k in outputparms}, "skipped")\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 582, in receive_output\n self.do_output_callback(final_output_callback)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 545, in do_output_callback\n final_output_callback(wo, self.processStatus)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 429, in receive_output\n output_callback(output, processStatus)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 1020, in loop_callback\n object_from_state(\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 391, in object_from_state\n raise WorkflowException(\ncwltool.errors.WorkflowException: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nDEBUG cwltool:workflow_job.py:564 [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/osmall": [\n 2\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/obig": [\n null\n ]\n}\nWARNING cwltool:workflow_job.py:570 [step loop] completed permanentFail\nERROR cwltool:workflow_job.py:520 [workflow ] Cannot collect workflow output: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nINFO cwltool:workflow_job.py:539 [workflow ] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow ] outputs null\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7mewqrkl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp45f8r8g2\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.0006661150000581983, 'start': 1685951439.112205, 'stop': 1685951439.112873, '$report_type': 'TestReport', 'item_index': 440, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_multi_source_loop_input_fail_no_requirement + location: ('tests/test_loop.py', 262, 'test_multi_source_loop_input_fail_no_requirement') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_default_value_loop + location: ('tests/test_loop.py', 272, 'test_default_value_loop') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_default_value_loop', 'location': ('tests/test_loop.py', 272, 'test_default_value_loop'), 'keywords': {'test_default_value_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002949979998447816, 'start': 1685951439.114215, 'stop': 1685951439.114511, '$report_type': 'TestReport', 'item_index': 441, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_value_from_fail_no_requirement', 'location': ('tests/test_loop.py', 200, 'test_loop_value_from_fail_no_requirement'), 'keywords': {'test_loop_value_from_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-value-from-loop-no-requirement.cwl:27:7: object id 'tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _9] start\n\x1b[1;30mINFO\x1b[0m [workflow _9] starting step subworkflow_4\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 1 completed success\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFailed to evaluate expression:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step subworkflow_4] Output of iteration 2 is missing expected field file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[step subworkflow_4] Iteration 2 completed permanentFail\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-value-from-loop-no-requirement.cwl:27:7: object id \'tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step subworkflow_4\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 1 completed success\nWARNING cwltool:command_line_tool.py:204 Failed to evaluate expression:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\nERROR cwltool:workflow_job.py:979 [step subworkflow_4] Output of iteration 2 is missing expected field file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_4] produced output {}\nWARNING cwltool:workflow_job.py:998 [step subworkflow_4] Iteration 2 completed permanentFail\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements')], 'duration': 0.9961248460003844, 'start': 1685951438.760916, 'stop': 1685951439.7570171, '$report_type': 'TestReport', 'item_index': 435, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_value_from_fail_no_requirement', 'location': ('tests/test_loop.py', 200, 'test_loop_value_from_fail_no_requirement'), 'keywords': {'test_loop_value_from_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-value-from-loop-no-requirement.cwl:27:7: object id 'tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _9] start\n\x1b[1;30mINFO\x1b[0m [workflow _9] starting step subworkflow_4\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 1 completed success\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFailed to evaluate expression:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step subworkflow_4] Output of iteration 2 is missing expected field file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[step subworkflow_4] Iteration 2 completed permanentFail\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-value-from-loop-no-requirement.cwl:27:7: object id \'tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step subworkflow_4\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 1 completed success\nWARNING cwltool:command_line_tool.py:204 Failed to evaluate expression:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\nERROR cwltool:workflow_job.py:979 [step subworkflow_4] Output of iteration 2 is missing expected field file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_4] produced output {}\nWARNING cwltool:workflow_job.py:998 [step subworkflow_4] Iteration 2 completed permanentFail\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements')], 'duration': 0.00036002799970447086, 'start': 1685951439.757768, 'stop': 1685951439.7581298, '$report_type': 'TestReport', 'item_index': 435, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_loop_value_from_fail_no_requirement + location: ('tests/test_loop.py', 200, 'test_loop_value_from_fail_no_requirement') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_loop_inside_scatter + location: ('tests/test_loop.py', 210, 'test_loop_inside_scatter') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_inside_scatter', 'location': ('tests/test_loop.py', 210, 'test_loop_inside_scatter'), 'keywords': {'test_loop_inside_scatter': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003171879998262739, 'start': 1685951439.75998, 'stop': 1685951439.760299, '$report_type': 'TestReport', 'item_index': 436, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps', 'location': ('tests/test_input_deps.py', 13, 'test_input_deps'), 'keywords': {'test_input_deps': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'")], 'duration': 0.8863417309994475, 'start': 1685951439.006012, 'stop': 1685951439.892333, '$report_type': 'TestReport', 'item_index': 387, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps', 'location': ('tests/test_input_deps.py', 13, 'test_input_deps'), 'keywords': {'test_input_deps': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'")], 'duration': 0.00023683100062044105, 'start': 1685951439.8928099, 'stop': 1685951439.893048, '$report_type': 'TestReport', 'item_index': 387, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_cmdline_opts', 'location': ('tests/test_input_deps.py', 43, 'test_input_deps_cmdline_opts'), 'keywords': {'test_input_deps_cmdline_opts': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00019443900055193808, 'start': 1685951439.8939362, 'stop': 1685951439.894132, '$report_type': 'TestReport', 'item_index': 388, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_input_deps.py::test_input_deps + location: ('tests/test_input_deps.py', 13, 'test_input_deps') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_input_deps.py::test_input_deps_cmdline_opts + location: ('tests/test_input_deps.py', 43, 'test_input_deps_cmdline_opts') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_when', 'location': ('tests/test_loop.py', 39, 'test_validate_loop_fail_when'), 'keywords': {'test_validate_loop_fail_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-when.cwl:32:11: object id \'tests/loop/invalid-loop-when.cwl#subworkflow/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\n Source is from conditional step and may produce `null`\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-when.cwl:18:3: The `cwltool:Loop` clause is not compatible with the `when`\n directive.\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-when.cwl:32:11: object id \'tests/loop/invalid-loop-when.cwl#subworkflow/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\n Source is from conditional step and may produce `null`\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-when.cwl:18:3: The `cwltool:Loop` clause is not compatible with the `when`\n directive.')], 'duration': 1.040507720000278, 'start': 1685951438.861541, 'stop': 1685951439.902024, '$report_type': 'TestReport', 'item_index': 421, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_when', 'location': ('tests/test_loop.py', 39, 'test_validate_loop_fail_when'), 'keywords': {'test_validate_loop_fail_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-when.cwl:32:11: object id \'tests/loop/invalid-loop-when.cwl#subworkflow/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\n Source is from conditional step and may produce `null`\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-when.cwl:18:3: The `cwltool:Loop` clause is not compatible with the `when`\n directive.\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-when.cwl:32:11: object id \'tests/loop/invalid-loop-when.cwl#subworkflow/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\n Source is from conditional step and may produce `null`\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-when.cwl:18:3: The `cwltool:Loop` clause is not compatible with the `when`\n directive.')], 'duration': 0.00021948999983578688, 'start': 1685951439.902556, 'stop': 1685951439.9027772, '$report_type': 'TestReport', 'item_index': 421, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_no_loop_when', 'location': ('tests/test_loop.py', 49, 'test_validate_loop_fail_no_loop_when'), 'keywords': {'test_validate_loop_fail_no_loop_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002804380001180107, 'start': 1685951439.9037492, 'stop': 1685951439.904031, '$report_type': 'TestReport', 'item_index': 422, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_no_loop_when + location: ('tests/test_loop.py', 49, 'test_validate_loop_fail_no_loop_when') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] +ut staging directory /private/tmp/docker_tmp1yceosyd +DEBUG cwltool:job.py:454 [job env.cwl_3] Removing temporary directory /private/tmp/docker_tmpgnhzumjf +DEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/do pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_default_value_loop', 'location': ('tests/test_loop.py', 272, 'test_default_value_loop'), 'keywords': {'test_default_value_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/default-value-loop.cwl:42:7: object id \'tests/loop/default-value-loop.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is used but only a single input source is\n declared\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _2] start\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step loop_2\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step big_values_2\n\x1b[1;30mINFO\x1b[0m [step big_values_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step big_values_3\n\x1b[1;30mINFO\x1b[0m [step big_values_3] start\n\x1b[1;30mINFO\x1b[0m [step big_values_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step big_values_4\n\x1b[1;30mINFO\x1b[0m [step big_values_4] start\n\x1b[1;30mINFO\x1b[0m [step big_values_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step big_values_5\n\x1b[1;30mINFO\x1b[0m [step big_values_5] start\n\x1b[1;30mINFO\x1b[0m [step big_values_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step big_values_6\n\x1b[1;30mINFO\x1b[0m [step big_values_6] start\n\x1b[1;30mINFO\x1b[0m [step big_values_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step big_values_7\n\x1b[1;30mINFO\x1b[0m [step big_values_7] start\n\x1b[1;30mINFO\x1b[0m [step big_values_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/default-value-loop.cwl:42:7: object id \'tests/loop/default-value-loop.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is used but only a single input source is\n declared\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step loop_2\nDEBUG cwltool:workflow_job.py:727 [step loop_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_2] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_2] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step big_values_2\nDEBUG cwltool:workflow_job.py:727 [step big_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_2] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_2] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_2] outputs {\n "o1": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_3] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_3] inputs {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step big_values_3\nDEBUG cwltool:workflow_job.py:727 [step big_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 5\n}\nINFO cwltool:workflow_job.py:75 [step big_values_3] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 8\n}\nINFO cwltool:workflow_job.py:572 [step big_values_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_3] outputs {\n "o1": 8\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_4] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_4] inputs {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step big_values_4\nDEBUG cwltool:workflow_job.py:727 [step big_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 8\n}\nINFO cwltool:workflow_job.py:75 [step big_values_4] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 11\n}\nINFO cwltool:workflow_job.py:572 [step big_values_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_4] outputs {\n "o1": 11\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 11\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_5] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_5] inputs {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step big_values_5\nDEBUG cwltool:workflow_job.py:727 [step big_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 11\n}\nINFO cwltool:workflow_job.py:75 [step big_values_5] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 14\n}\nINFO cwltool:workflow_job.py:572 [step big_values_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_5] outputs {\n "o1": 14\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 14\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_6] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_6] inputs {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step big_values_6\nDEBUG cwltool:workflow_job.py:727 [step big_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 14\n}\nINFO cwltool:workflow_job.py:75 [step big_values_6] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 17\n}\nINFO cwltool:workflow_job.py:572 [step big_values_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_6] outputs {\n "o1": 17\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 17\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_7] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_7] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_7] inputs {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step big_values_7\nDEBUG cwltool:workflow_job.py:727 [step big_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 17\n}\nINFO cwltool:workflow_job.py:75 [step big_values_7] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 20\n}\nINFO cwltool:workflow_job.py:572 [step big_values_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_7] outputs {\n "o1": 20\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 20\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 6 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop_2] loop condition $(inputs.i1 < 20) evaluated to False at iteration 6\nDEBUG cwltool:workflow_job.py:925 [step loop_2] inputs was {\n "i1": 20\n}\nDEBUG cwltool:workflow_job.py:564 [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": [\n null,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {\n "o1": [\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpoar6z8_e\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2uugk7_4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpgertiuxv\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr7t2byqk\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwr14e3q7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo4__2eh4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5y1ls9r3\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1016340950000085, 'start': 1685951439.114841, 'stop': 1685951440.216449, '$report_type': 'TestReport', 'item_index': 441, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_default_value_loop', 'location': ('tests/test_loop.py', 272, 'test_default_value_loop'), 'keywords': {'test_default_value_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/default-value-loop.cwl:42:7: object id \'tests/loop/default-value-loop.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is used but only a single input source is\n declared\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _2] start\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step loop_2\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step big_values_2\n\x1b[1;30mINFO\x1b[0m [step big_values_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step big_values_3\n\x1b[1;30mINFO\x1b[0m [step big_values_3] start\n\x1b[1;30mINFO\x1b[0m [step big_values_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step big_values_4\n\x1b[1;30mINFO\x1b[0m [step big_values_4] start\n\x1b[1;30mINFO\x1b[0m [step big_values_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step big_values_5\n\x1b[1;30mINFO\x1b[0m [step big_values_5] start\n\x1b[1;30mINFO\x1b[0m [step big_values_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step big_values_6\n\x1b[1;30mINFO\x1b[0m [step big_values_6] start\n\x1b[1;30mINFO\x1b[0m [step big_values_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step big_values_7\n\x1b[1;30mINFO\x1b[0m [step big_values_7] start\n\x1b[1;30mINFO\x1b[0m [step big_values_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/default-value-loop.cwl:42:7: object id \'tests/loop/default-value-loop.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is used but only a single input source is\n declared\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step loop_2\nDEBUG cwltool:workflow_job.py:727 [step loop_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_2] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_2] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step big_values_2\nDEBUG cwltool:workflow_job.py:727 [step big_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_2] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_2] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_2] outputs {\n "o1": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_3] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_3] inputs {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step big_values_3\nDEBUG cwltool:workflow_job.py:727 [step big_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 5\n}\nINFO cwltool:workflow_job.py:75 [step big_values_3] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 8\n}\nINFO cwltool:workflow_job.py:572 [step big_values_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_3] outputs {\n "o1": 8\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_4] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_4] inputs {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step big_values_4\nDEBUG cwltool:workflow_job.py:727 [step big_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 8\n}\nINFO cwltool:workflow_job.py:75 [step big_values_4] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 11\n}\nINFO cwltool:workflow_job.py:572 [step big_values_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_4] outputs {\n "o1": 11\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 11\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_5] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_5] inputs {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step big_values_5\nDEBUG cwltool:workflow_job.py:727 [step big_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 11\n}\nINFO cwltool:workflow_job.py:75 [step big_values_5] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 14\n}\nINFO cwltool:workflow_job.py:572 [step big_values_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_5] outputs {\n "o1": 14\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 14\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_6] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_6] inputs {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step big_values_6\nDEBUG cwltool:workflow_job.py:727 [step big_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 14\n}\nINFO cwltool:workflow_job.py:75 [step big_values_6] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 17\n}\nINFO cwltool:workflow_job.py:572 [step big_values_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_6] outputs {\n "o1": 17\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 17\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_7] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_7] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_7] inputs {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step big_values_7\nDEBUG cwltool:workflow_job.py:727 [step big_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 17\n}\nINFO cwltool:workflow_job.py:75 [step big_values_7] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 20\n}\nINFO cwltool:workflow_job.py:572 [step big_values_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_7] outputs {\n "o1": 20\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 20\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 6 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop_2] loop condition $(inputs.i1 < 20) evaluated to False at iteration 6\nDEBUG cwltool:workflow_job.py:925 [step loop_2] inputs was {\n "i1": 20\n}\nDEBUG cwltool:workflow_job.py:564 [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": [\n null,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {\n "o1": [\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpoar6z8_e\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2uugk7_4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpgertiuxv\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr7t2byqk\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwr14e3q7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo4__2eh4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5y1ls9r3\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00047727000037411926, 'start': 1685951440.2176561, 'stop': 1685951440.218135, '$report_type': 'TestReport', 'item_index': 441, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_make_template.py::test_anonymous_record', 'location': ('tests/test_make_template.py', 7, 'test_anonymous_record'), 'keywords': {'test_anonymous_record': 1, 'test_make_template.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00027614000009634765, 'start': 1685951440.219937, 'stop': 1685951440.2202141, '$report_type': 'TestReport', 'item_index': 442, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_default_value_loop + location: ('tests/test_loop.py', 272, 'test_default_value_loop') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_make_template.py::test_anonymous_record + location: ('tests/test_make_template.py', 7, 'test_anonymous_record') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_make_template.py::test_anonymous_record', 'location': ('tests/test_make_template.py', 7, 'test_anonymous_record'), 'keywords': {'test_anonymous_record': 1, 'test_make_template.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000529472999915015, 'start': 1685951440.220674, 'stop': 1685951440.221205, '$report_type': 'TestReport', 'item_index': 442, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_make_template.py::test_anonymous_record', 'location': ('tests/test_make_template.py', 7, 'test_anonymous_record'), 'keywords': {'test_anonymous_record': 1, 'test_make_template.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003409410001040669, 'start': 1685951440.221874, 'stop': 1685951440.2222168, '$report_type': 'TestReport', 'item_index': 442, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_make_template.py::test_anonymous_record + location: ('tests/test_make_template.py', 7, 'test_anonymous_record') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_make_template.py::test_union + location: ('tests/test_make_template.py', 12, 'test_union') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_make_template.py::test_union', 'location': ('tests/test_make_template.py', 12, 'test_union'), 'keywords': {'test_union': 1, 'test_make_template.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00031190899971988983, 'start': 1685951440.223593, 'stop': 1685951440.223907, '$report_type': 'TestReport', 'item_index': 443, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_make_template.py::test_union', 'location': ('tests/test_make_template.py', 12, 'test_union'), 'keywords': {'test_union': 1, 'test_make_template.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006343559998640558, 'start': 1685951440.224712, 'stop': 1685951440.2253492, '$report_type': 'TestReport', 'item_index': 443, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_make_template.py::test_union', 'location': ('tests/test_make_template.py', 12, 'test_union'), 'keywords': {'test_union': 1, 'test_make_template.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00023415800023940392, 'start': 1685951440.225804, 'stop': 1685951440.2260401, '$report_type': 'TestReport', 'item_index': 443, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_make_template.py::test_union + location: ('tests/test_make_template.py', 12, 'test_union') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_make_template.py::test_optional_union + location: ('tests/test_make_template.py', 21, 'test_optional_union') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_make_template.py::test_optional_union', 'location': ('tests/test_make_template.py', 21, 'test_optional_union'), 'keywords': {'test_optional_union': 1, 'test_make_template.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00020456899983400945, 'start': 1685951440.22694, 'stop': 1685951440.227145, '$report_type': 'TestReport', 'item_index': 444, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_make_template.py::test_optional_union', 'location': ('tests/test_make_template.py', 21, 'test_optional_union'), 'keywords': {'test_optional_union': 1, 'test_make_template.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003357499999765423, 'start': 1685951440.2274702, 'stop': 1685951440.227807, '$report_type': 'TestReport', 'item_index': 444, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_make_template.py::test_optional_union', 'location': ('tests/test_make_template.py', 21, 'test_optional_union'), 'keywords': {'test_optional_union': 1, 'test_make_template.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000201687000298989, 'start': 1685951440.228336, 'stop': 1685951440.228539, '$report_type': 'TestReport', 'item_index': 444, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_make_template.py::test_optional_union + location: ('tests/test_make_template.py', 21, 'test_optional_union') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_version', 'location': ('tests/test_misc_cli.py', 7, 'test_version'), 'keywords': {'test_version': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004536540000117384, 'start': 1685951440.229677, 'stop': 1685951440.2301319, '$report_type': 'TestReport', 'item_index': 445, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_misc_cli.py::test_version + location: ('tests/test_misc_cli.py', 7, 'test_version') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_version', 'location': ('tests/test_misc_cli.py', 7, 'test_version'), 'keywords': {'test_version': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.008849422999446688, 'start': 1685951440.230711, 'stop': 1685951440.239562, '$report_type': 'TestReport', 'item_index': 445, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_version', 'location': ('tests/test_misc_cli.py', 7, 'test_version'), 'keywords': {'test_version': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002790590006043203, 'start': 1685951440.240109, 'stop': 1685951440.2403898, '$report_type': 'TestReport', 'item_index': 445, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_misc_cli.py::test_version + location: ('tests/test_misc_cli.py', 7, 'test_version') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_misc_cli.py::test_print_supported_versions + location: ('tests/test_misc_cli.py', 14, 'test_print_supported_versions') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_print_supported_versions', 'location': ('tests/test_misc_cli.py', 14, 'test_print_supported_versions'), 'keywords': {'test_print_supported_versions': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002298580002388917, 'start': 1685951440.241565, 'stop': 1685951440.241796, '$report_type': 'TestReport', 'item_index': 446, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_print_supported_versions', 'location': ('tests/test_misc_cli.py', 14, 'test_print_supported_versions'), 'keywords': {'test_print_supported_versions': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1')], 'duration': 0.008608372999333369, 'start': 1685951440.242142, 'stop': 1685951440.250751, '$report_type': 'TestReport', 'item_index': 446, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_print_supported_versions', 'location': ('tests/test_misc_cli.py', 14, 'test_print_supported_versions'), 'keywords': {'test_print_supported_versions': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1')], 'duration': 0.00027047300045524025, 'start': 1685951440.251284, 'stop': 1685951440.2515562, '$report_type': 'TestReport', 'item_index': 446, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_misc_cli.py::test_print_supported_versions + location: ('tests/test_misc_cli.py', 14, 'test_print_supported_versions') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_misc_cli.py::test_empty_cmdling + location: ('tests/test_misc_cli.py', 21, 'test_empty_cmdling') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_empty_cmdling', 'location': ('tests/test_misc_cli.py', 21, 'test_empty_cmdling'), 'keywords': {'test_empty_cmdling': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00022971899943513563, 'start': 1685951440.252862, 'stop': 1685951440.253093, '$report_type': 'TestReport', 'item_index': 447, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_empty_cmdling', 'location': ('tests/test_misc_cli.py', 21, 'test_empty_cmdling'), 'keywords': {'test_empty_cmdling': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nERROR cwltool:main.py:1037 CWL document required, no input file was provided')], 'duration': 0.016150884999660775, 'start': 1685951440.2536252, 'stop': 1685951440.2697768, '$report_type': 'TestReport', 'item_index': 447, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_empty_cmdling', 'location': ('tests/test_misc_cli.py', 21, 'test_empty_cmdling'), 'keywords': {'test_empty_cmdling': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nERROR cwltool:main.py:1037 CWL document required, no input file was provided')], 'duration': 0.00021182300042710267, 'start': 1685951440.270251, 'stop': 1685951440.270464, '$report_type': 'TestReport', 'item_index': 447, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_tool_help', 'location': ('tests/test_misc_cli.py', 28, 'test_tool_help'), 'keywords': {'test_tool_help': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00028088700037187664, 'start': 1685951440.271307, 'stop': 1685951440.27159, '$report_type': 'TestReport', 'item_index': 448, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_misc_cli.py::test_empty_cmdling + location: ('tests/test_misc_cli.py', 21, 'test_empty_cmdling') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_misc_cli.py::test_tool_help + location: ('tests/test_misc_cli.py', 28, 'test_tool_help') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_file_overwrite_without_ext', 'location': ('tests/test_ext.py', 106, 'test_disable_file_overwrite_without_ext'), 'keywords': {'test_disable_file_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl'\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] /private/tmp/docker_tmpbn74w3_i$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpbn74w3_i,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdihp24br,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py,readonly \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpyjmpwq8v/20230605095039-365737.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl",\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value"\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updateval.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updateval.cwl] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "size": 102,\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updateval.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updateval.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job updateval.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updateval.cwl] /private/tmp/docker_tmpbn74w3_i$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpbn74w3_i,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdihp24br,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py,readonly \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpyjmpwq8v/20230605095039-365737.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py \\\n value\nINFO cwltool:job.py:905 [job updateval.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job updateval.cwl] completed success\nDEBUG cwltool:job.py:422 [job updateval.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpbn74w3_i/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job updateval.cwl] Removing input staging directory /private/tmp/docker_tmpysfywzqb\nDEBUG cwltool:job.py:454 [job updateval.cwl] Removing temporary directory /private/tmp/docker_tmpdihp24br\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpbn74w3_i/value to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbn74w3_i\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.741776122000374, 'start': 1685951438.650143, 'stop': 1685951440.3918788, '$report_type': 'TestReport', 'item_index': 370, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_file_overwrite_without_ext', 'location': ('tests/test_ext.py', 106, 'test_disable_file_overwrite_without_ext'), 'keywords': {'test_disable_file_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl'\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] /private/tmp/docker_tmpbn74w3_i$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpbn74w3_i,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdihp24br,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py,readonly \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpyjmpwq8v/20230605095039-365737.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl",\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value"\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updateval.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updateval.cwl] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "size": 102,\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updateval.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updateval.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job updateval.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updateval.cwl] /private/tmp/docker_tmpbn74w3_i$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpbn74w3_i,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdihp24br,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py,readonly \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpyjmpwq8v/20230605095039-365737.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py \\\n value\nINFO cwltool:job.py:905 [job updateval.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job updateval.cwl] completed success\nDEBUG cwltool:job.py:422 [job updateval.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpbn74w3_i/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job updateval.cwl] Removing input staging directory /private/tmp/docker_tmpysfywzqb\nDEBUG cwltool:job.py:454 [job updateval.cwl] Removing temporary directory /private/tmp/docker_tmpdihp24br\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpbn74w3_i/value to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbn74w3_i\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008024259996091132, 'start': 1685951440.393035, 'stop': 1685951440.3938391, '$report_type': 'TestReport', 'item_index': 370, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_disable_file_overwrite_without_ext + location: ('tests/test_ext.py', 106, 'test_disable_file_overwrite_without_ext') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_ext.py::test_disable_dir_overwrite_without_ext + location: ('tests/test_ext.py', 142, 'test_disable_dir_overwrite_without_ext') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_dir_overwrite_without_ext', 'location': ('tests/test_ext.py', 142, 'test_disable_dir_overwrite_without_ext'), 'keywords': {'test_disable_dir_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0019440989999566227, 'start': 1685951440.3958342, 'stop': 1685951440.39778, '$report_type': 'TestReport', 'item_index': 371, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel --debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel --debug]'), 'keywords': {'test_cache_relative_paths[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_7] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_7] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_7] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_7] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmppgt8gdo1/stg66bad48d-a7d9-4436-b9e8-a77b91febaac/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmppgt8gdo1/stg66bad48d-a7d9-4436-b9e8-a77b91febaac/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(secondary-files.cwl_7), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job secondary-files.cwl_7] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_7] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_7] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_7] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_7] Removing input staging directory /private/tmp/docker_tmppgt8gdo1\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_7] Removing temporary directory /private/tmp/docker_tmp9xbgk171\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cacheja0eo8kh\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_8] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_8] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache1e8ss_pv\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.110423813000125, 'start': 1685951438.560262, 'stop': 1685951440.670636, '$report_type': 'TestReport', 'item_index': 303, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel --debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel --debug]'), 'keywords': {'test_cache_relative_paths[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_7] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_7] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_7] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_7] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmppgt8gdo1/stg66bad48d-a7d9-4436-b9e8-a77b91febaac/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmppgt8gdo1/stg66bad48d-a7d9-4436-b9e8-a77b91febaac/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(secondary-files.cwl_7), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job secondary-files.cwl_7] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_7] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_7] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_7] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_7] Removing input staging directory /private/tmp/docker_tmppgt8gdo1\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_7] Removing temporary directory /private/tmp/docker_tmp9xbgk171\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cacheja0eo8kh\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_8] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_8] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache1e8ss_pv\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0009610970000721863, 'start': 1685951440.6720278, 'stop': 1685951440.672991, '$report_type': 'TestReport', 'item_index': 303, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cache_relative_paths[--parallel --debug] + location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel --debug]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_write_summary + location: ('tests/test_examples.py', 1326, 'test_write_summary') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_write_summary', 'location': ('tests/test_examples.py', 1326, 'test_write_summary'), 'keywords': {'test_write_summary': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0024757220007813885, 'start': 1685951440.675128, 'stop': 1685951440.6776068, '$report_type': 'TestReport', 'item_index': 304, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_cmdline_opts', 'location': ('tests/test_input_deps.py', 43, 'test_input_deps_cmdline_opts'), 'keywords': {'test_input_deps_cmdline_opts': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}')], 'duration': 0.8830137269997067, 'start': 1685951439.894478, 'stop': 1685951440.777471, '$report_type': 'TestReport', 'item_index': 388, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_cmdline_opts', 'location': ('tests/test_input_deps.py', 43, 'test_input_deps_cmdline_opts'), 'keywords': {'test_input_deps_cmdline_opts': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}')], 'duration': 0.00019988900021417066, 'start': 1685951440.7779331, 'stop': 1685951440.778133, '$report_type': 'TestReport', 'item_index': 388, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_input_deps.py::test_input_deps_cmdline_opts + location: ('tests/test_input_deps.py', 43, 'test_input_deps_cmdline_opts') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_cmdline_opts_relative_deps_cwd', 'location': ('tests/test_input_deps.py', 73, 'test_input_deps_cmdline_opts_relative_deps_cwd'), 'keywords': {'test_input_deps_cmdline_opts_relative_deps_cwd': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00019219400019210298, 'start': 1685951440.779031, 'stop': 1685951440.7792242, '$report_type': 'TestReport', 'item_index': 389, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_input_deps.py::test_input_deps_cmdline_opts_relative_deps_cwd + location: ('tests/test_input_deps.py', 73, 'test_input_deps_cmdline_opts_relative_deps_cwd') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_no_loop_when', 'location': ('tests/test_loop.py', 49, 'test_validate_loop_fail_no_loop_when'), 'keywords': {'test_validate_loop_fail_no_loop_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-no-loopWhen.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-no-loopWhen.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-no-loopWhen.cwl:31:11: object id 'tests/loop/invalid-no-loopWhen.cwl#subworkflow/i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-no-loopWhen.cwl:2:1: Object 'tests/loop/invalid-no-loopWhen.cwl' is not valid\n because\n tried 'Workflow' but\ntests/loop/invalid-no-loopWhen.cwl:17:1: the 'steps' field is not valid because\n tried array of but\ntests/loop/invalid-no-loopWhen.cwl:18:3: item is invalid because\ntests/loop/invalid-no-loopWhen.cwl:28:5: the 'requirements' field is not valid because\n tried array of but\ntests/loop/invalid-no-loopWhen.cwl:29:7: item is invalid because\n missing required field 'loopWhen'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-no-loopWhen.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-no-loopWhen.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-no-loopWhen.cwl:31:11: object id 'tests/loop/invalid-no-loopWhen.cwl#subworkflow/i1' previously defined\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-no-loopWhen.cwl:2:1: Object 'tests/loop/invalid-no-loopWhen.cwl' is not valid\n because\n tried 'Workflow' but\ntests/loop/invalid-no-loopWhen.cwl:17:1: the 'steps' field is not valid because\n tried array of but\ntests/loop/invalid-no-loopWhen.cwl:18:3: item is invalid because\ntests/loop/invalid-no-loopWhen.cwl:28:5: the 'requirements' field is not valid because\n tried array of but\ntests/loop/invalid-no-loopWhen.cwl:29:7: item is invalid because\n missing required field 'loopWhen'")], 'duration': 1.0394022939999559, 'start': 1685951439.904522, 'stop': 1685951440.943899, '$report_type': 'TestReport', 'item_index': 422, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_no_loop_when', 'location': ('tests/test_loop.py', 49, 'test_validate_loop_fail_no_loop_when'), 'keywords': {'test_validate_loop_fail_no_loop_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-no-loopWhen.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-no-loopWhen.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-no-loopWhen.cwl:31:11: object id 'tests/loop/invalid-no-loopWhen.cwl#subworkflow/i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-no-loopWhen.cwl:2:1: Object 'tests/loop/invalid-no-loopWhen.cwl' is not valid\n because\n tried 'Workflow' but\ntests/loop/invalid-no-loopWhen.cwl:17:1: the 'steps' field is not valid because\n tried array of but\ntests/loop/invalid-no-loopWhen.cwl:18:3: item is invalid because\ntests/loop/invalid-no-loopWhen.cwl:28:5: the 'requirements' field is not valid because\n tried array of but\ntests/loop/invalid-no-loopWhen.cwl:29:7: item is invalid because\n missing required field 'loopWhen'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-no-loopWhen.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-no-loopWhen.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-no-loopWhen.cwl:31:11: object id 'tests/loop/invalid-no-loopWhen.cwl#subworkflow/i1' previously defined\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-no-loopWhen.cwl:2:1: Object 'tests/loop/invalid-no-loopWhen.cwl' is not valid\n because\n tried 'Workflow' but\ntests/loop/invalid-no-loopWhen.cwl:17:1: the 'steps' field is not valid because\n tried array of but\ntests/loop/invalid-no-loopWhen.cwl:18:3: item is invalid because\ntests/loop/invalid-no-loopWhen.cwl:28:5: the 'requirements' field is not valid because\n tried array of but\ntests/loop/invalid-no-loopWhen.cwl:29:7: item is invalid because\n missing required field 'loopWhen'")], 'duration': 0.00021394800023699645, 'start': 1685951440.944436, 'stop': 1685951440.9446511, '$report_type': 'TestReport', 'item_index': 422, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_workflow', 'location': ('tests/test_loop.py', 59, 'test_validate_loop_fail_on_workflow'), 'keywords': {'test_validate_loop_fail_on_workflow': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00021646400000463473, 'start': 1685951440.9457228, 'stop': 1685951440.945941, '$report_type': 'TestReport', 'item_index': 423, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_no_loop_when + location: ('tests/test_loop.py', 49, 'test_validate_loop_fail_no_loop_when') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_on_workflow + location: ('tests/test_loop.py', 59, 'test_validate_loop_fail_on_workflow') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_tool_help', 'location': ('tests/test_misc_cli.py', 28, 'test_tool_help'), 'keywords': {'test_tool_help': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl'")], 'duration': 0.7921529449995433, 'start': 1685951440.272054, 'stop': 1685951441.064188, '$report_type': 'TestReport', 'item_index': 448, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_tool_help', 'location': ('tests/test_misc_cli.py', 28, 'test_tool_help'), 'keywords': {'test_tool_help': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl'")], 'duration': 0.0002034640001511434, 'start': 1685951441.064787, 'stop': 1685951441.064992, '$report_type': 'TestReport', 'item_index': 448, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_misc_cli.py::test_tool_help + location: ('tests/test_misc_cli.py', 28, 'test_tool_help') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_misc_cli.py::test_basic_pack + location: ('tests/test_misc_cli.py', 35, 'test_basic_pack') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_basic_pack', 'location': ('tests/test_misc_cli.py', 35, 'test_basic_pack'), 'keywords': {'test_basic_pack': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00019015100042452104, 'start': 1685951441.065817, 'stop': 1685951441.066008, '$report_type': 'TestReport', 'item_index': 449, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_inside_scatter', 'location': ('tests/test_loop.py', 210, 'test_loop_inside_scatter'), 'keywords': {'test_loop_inside_scatter': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/loop-inside-scatter.cwl:40:13: object id 'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1' previously defined\ntests/loop/loop-inside-scatter.cwl:40:13: object id 'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _10] start\n\x1b[1;30mINFO\x1b[0m [workflow _10] starting step scatter\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter] starting step subworkflow_5\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_2] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_2] starting step subworkflow_6\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_2] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] starting step subworkflow_7\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] starting step subworkflow_8\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] starting step subworkflow_9\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _10] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-scatter.cwl:40:13: object id \'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-scatter.cwl:40:13: object id \'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {\n "i1": [\n 1,\n 2,\n 3,\n 4,\n 5\n ],\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step scatter\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter] starting step subworkflow_5\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_5] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_5] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_2] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_2] inputs {\n "i1": 2,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_2] starting step subworkflow_6\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 8 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_6] loop condition $(inputs.i1 < 10) evaluated to False at iteration 8\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_6] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_2] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_3] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_3] inputs {\n "i1": 3,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_3] starting step subworkflow_7\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 7 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_7] loop condition $(inputs.i1 < 10) evaluated to False at iteration 7\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_7] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_3] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_4] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_4] inputs {\n "i1": 4,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_4] starting step subworkflow_8\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_8] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 6 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_8] loop condition $(inputs.i1 < 10) evaluated to False at iteration 6\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_8] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_8] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_4] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_5] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_5] inputs {\n "i1": 5,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_5] starting step subworkflow_9\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 5 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_9] loop condition $(inputs.i1 < 10) evaluated to False at iteration 5\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_9] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_9] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_5] outputs {\n "o1": 10\n}\nDEBUG cwltool:workflow_job.py:564 [step scatter] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/o1": [\n 10,\n 10,\n 10,\n 10,\n 10\n ]\n}\nINFO cwltool:workflow_job.py:572 [step scatter] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {\n "o1": [\n 10,\n 10,\n 10,\n 10,\n 10\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3toza5rh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa65hoj0o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp09jo_4c_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1vhvuysq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo6sf1hnz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5og7ngfg\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.3274409570003627, 'start': 1685951439.760791, 'stop': 1685951441.088199, '$report_type': 'TestReport', 'item_index': 436, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_inside_scatter', 'location': ('tests/test_loop.py', 210, 'test_loop_inside_scatter'), 'keywords': {'test_loop_inside_scatter': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/loop-inside-scatter.cwl:40:13: object id 'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1' previously defined\ntests/loop/loop-inside-scatter.cwl:40:13: object id 'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _10] start\n\x1b[1;30mINFO\x1b[0m [workflow _10] starting step scatter\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter] starting step subworkflow_5\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_2] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_2] starting step subworkflow_6\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_2] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] starting step subworkflow_7\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] starting step subworkflow_8\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] starting step subworkflow_9\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _10] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-scatter.cwl:40:13: object id \'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-scatter.cwl:40:13: object id \'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {\n "i1": [\n 1,\n 2,\n 3,\n 4,\n 5\n ],\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step scatter\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter] starting step subworkflow_5\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_5] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_5] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_2] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_2] inputs {\n "i1": 2,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_2] starting step subworkflow_6\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 8 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_6] loop condition $(inputs.i1 < 10) evaluated to False at iteration 8\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_6] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_2] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_3] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_3] inputs {\n "i1": 3,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_3] starting step subworkflow_7\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 7 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_7] loop condition $(inputs.i1 < 10) evaluated to False at iteration 7\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_7] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_3] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_4] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_4] inputs {\n "i1": 4,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_4] starting step subworkflow_8\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_8] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 6 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_8] loop condition $(inputs.i1 < 10) evaluated to False at iteration 6\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_8] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_8] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_4] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_5] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_5] inputs {\n "i1": 5,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_5] starting step subworkflow_9\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 5 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_9] loop condition $(inputs.i1 < 10) evaluated to False at iteration 5\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_9] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_9] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_5] outputs {\n "o1": 10\n}\nDEBUG cwltool:workflow_job.py:564 [step scatter] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/o1": [\n 10,\n 10,\n 10,\n 10,\n 10\n ]\n}\nINFO cwltool:workflow_job.py:572 [step scatter] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {\n "o1": [\n 10,\n 10,\n 10,\n 10,\n 10\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3toza5rh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa65hoj0o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp09jo_4c_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1vhvuysq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo6sf1hnz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5og7ngfg\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006262719998630928, 'start': 1685951441.089491, 'stop': 1685951441.090119, '$report_type': 'TestReport', 'item_index': 436, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_nested_loops', 'location': ('tests/test_loop.py', 223, 'test_nested_loops'), 'keywords': {'test_nested_loops': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00025334400015708525, 'start': 1685951441.091902, 'stop': 1685951441.092157, '$report_type': 'TestReport', 'item_index': 437, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_loop_inside_scatter + location: ('tests/test_loop.py', 210, 'test_loop_inside_scatter') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_nested_loops + location: ('tests/test_loop.py', 223, 'test_nested_loops') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]'), 'keywords': {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task1_10\nDEBUG cwltool:workflow_job.py:727 [step task1_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_10\nDEBUG cwltool:command_line_tool.py:988 [job task1_8] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_8] initial work dir {}\nINFO cwltool:job.py:266 [job task1_8] /private/tmp/docker_tmpqd0zbt01$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqd0zbt01,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwbwvw4vq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095039-089090.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_8] completed success\nDEBUG cwltool:job.py:422 [job task1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqd0zbt01/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_10] completed success\nDEBUG cwltool:job.py:446 [job task1_8] Removing input staging directory /private/tmp/docker_tmpsuq2jbza\nDEBUG cwltool:job.py:454 [job task1_8] Removing temporary directory /private/tmp/docker_tmpwbwvw4vq\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task2_10\nDEBUG cwltool:workflow_job.py:727 [step task2_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_10\nDEBUG cwltool:command_line_tool.py:988 [job task2_8] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_8] initial work dir {}\nINFO cwltool:job.py:266 [job task2_8] /private/tmp/docker_tmpukxzzulb$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpukxzzulb,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp460y3fko,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095040-128027.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_8] completed success\nDEBUG cwltool:job.py:422 [job task2_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpukxzzulb/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_10] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {}\nDEBUG cwltool:job.py:446 [job task2_8] Removing input staging directory /private/tmp/docker_tmp0ewn2kda\nDEBUG cwltool:job.py:454 [job task2_8] Removing temporary directory /private/tmp/docker_tmp460y3fko\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpukxzzulb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqd0zbt01\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6qs7k1_4\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 3.6632841119999284, 'start': 1685951437.4933639, 'stop': 1685951441.156561, '$report_type': 'TestReport', 'item_index': 276, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]'), 'keywords': {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task1_10\nDEBUG cwltool:workflow_job.py:727 [step task1_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_10\nDEBUG cwltool:command_line_tool.py:988 [job task1_8] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_8] initial work dir {}\nINFO cwltool:job.py:266 [job task1_8] /private/tmp/docker_tmpqd0zbt01$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqd0zbt01,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwbwvw4vq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095039-089090.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_8] completed success\nDEBUG cwltool:job.py:422 [job task1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqd0zbt01/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_10] completed success\nDEBUG cwltool:job.py:446 [job task1_8] Removing input staging directory /private/tmp/docker_tmpsuq2jbza\nDEBUG cwltool:job.py:454 [job task1_8] Removing temporary directory /private/tmp/docker_tmpwbwvw4vq\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task2_10\nDEBUG cwltool:workflow_job.py:727 [step task2_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_10\nDEBUG cwltool:command_line_tool.py:988 [job task2_8] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_8] initial work dir {}\nINFO cwltool:job.py:266 [job task2_8] /private/tmp/docker_tmpukxzzulb$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpukxzzulb,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp460y3fko,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095040-128027.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_8] completed success\nDEBUG cwltool:job.py:422 [job task2_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpukxzzulb/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_10] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {}\nDEBUG cwltool:job.py:446 [job task2_8] Removing input staging directory /private/tmp/docker_tmp0ewn2kda\nDEBUG cwltool:job.py:454 [job task2_8] Removing temporary directory /private/tmp/docker_tmp460y3fko\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpukxzzulb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqd0zbt01\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6qs7k1_4\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008422430000791792, 'start': 1685951441.1581, 'stop': 1685951441.158945, '$report_type': 'TestReport', 'item_index': 276, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]'), 'keywords': {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0020675499999924796, 'start': 1685951441.160426, 'stop': 1685951441.162495, '$report_type': 'TestReport', 'item_index': 277, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_dir_overwrite_without_ext', 'location': ('tests/test_ext.py', 142, 'test_disable_dir_overwrite_without_ext'), 'keywords': {'test_disable_dir_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp",\n "basename": "inp",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp/blurb",\n "basename": "blurb",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp/blurb"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl'\n\x1b[1;30mINFO\x1b[0m [job updatedir.cwl] /private/tmp/docker_tmp9bw9d8xw$ touch \\\n inp/blurb\n\x1b[1;30mINFO\x1b[0m [job updatedir.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl",\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updatedir.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updatedir.cwl] {\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "basename": "tmp",\n "listing": []\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updatedir.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "/private/tmp/docker_tmp9bw9d8xw/inp",\n "WritableDirectory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updatedir.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp/blurb"\n }\n]\nDEBUG cwltool:job.py:215 [job updatedir.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "/private/tmp/docker_tmp9bw9d8xw/inp",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updatedir.cwl] /private/tmp/docker_tmp9bw9d8xw$ touch \\\n inp/blurb\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job updatedir.cwl] completed success\nDEBUG cwltool:job.py:422 [job updatedir.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9bw9d8xw/inp",\n "basename": "inp",\n "nameroot": "inp",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job updatedir.cwl] Removing input staging directory /private/tmp/docker_tmpg93e0s32\nDEBUG cwltool:job.py:454 [job updatedir.cwl] Removing temporary directory /private/tmp/docker_tmp6xesz114\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp9bw9d8xw/inp to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9bw9d8xw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7997955589999037, 'start': 1685951440.398328, 'stop': 1685951441.198105, '$report_type': 'TestReport', 'item_index': 371, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_dir_overwrite_without_ext', 'location': ('tests/test_ext.py', 142, 'test_disable_dir_overwrite_without_ext'), 'keywords': {'test_disable_dir_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp",\n "basename": "inp",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp/blurb",\n "basename": "blurb",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp/blurb"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl'\n\x1b[1;30mINFO\x1b[0m [job updatedir.cwl] /private/tmp/docker_tmp9bw9d8xw$ touch \\\n inp/blurb\n\x1b[1;30mINFO\x1b[0m [job updatedir.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl",\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updatedir.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updatedir.cwl] {\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "basename": "tmp",\n "listing": []\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updatedir.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "/private/tmp/docker_tmp9bw9d8xw/inp",\n "WritableDirectory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updatedir.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp/blurb"\n }\n]\nDEBUG cwltool:job.py:215 [job updatedir.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "/private/tmp/docker_tmp9bw9d8xw/inp",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updatedir.cwl] /private/tmp/docker_tmp9bw9d8xw$ touch \\\n inp/blurb\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job updatedir.cwl] completed success\nDEBUG cwltool:job.py:422 [job updatedir.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9bw9d8xw/inp",\n "basename": "inp",\n "nameroot": "inp",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job updatedir.cwl] Removing input staging directory /private/tmp/docker_tmpg93e0s32\nDEBUG cwltool:job.py:454 [job updatedir.cwl] Removing temporary directory /private/tmp/docker_tmp6xesz114\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp9bw9d8xw/inp to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9bw9d8xw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007611159999214578, 'start': 1685951441.199606, 'stop': 1685951441.200369, '$report_type': 'TestReport', 'item_index': 371, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_disable_dir_overwrite_without_ext + location: ('tests/test_ext.py', 142, 'test_disable_dir_overwrite_without_ext') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_ext.py::test_disable_file_creation_in_outdir_with_ext + location: ('tests/test_ext.py', 155, 'test_disable_file_creation_in_outdir_with_ext') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_file_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 155, 'test_disable_file_creation_in_outdir_with_ext'), 'keywords': {'test_disable_file_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013144630001988844, 'start': 1685951441.2017689, 'stop': 1685951441.203084, '$report_type': 'TestReport', 'item_index': 372, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_cmdline_opts_relative_deps_cwd', 'location': ('tests/test_input_deps.py', 73, 'test_input_deps_cmdline_opts_relative_deps_cwd'), 'keywords': {'test_input_deps_cmdline_opts_relative_deps_cwd': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}')], 'duration': 0.7899493630002326, 'start': 1685951440.779573, 'stop': 1685951441.569504, '$report_type': 'TestReport', 'item_index': 389, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_cmdline_opts_relative_deps_cwd', 'location': ('tests/test_input_deps.py', 73, 'test_input_deps_cmdline_opts_relative_deps_cwd'), 'keywords': {'test_input_deps_cmdline_opts_relative_deps_cwd': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}')], 'duration': 0.00020822599981329404, 'start': 1685951441.5699599, 'stop': 1685951441.570169, '$report_type': 'TestReport', 'item_index': 389, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_secondary_files', 'location': ('tests/test_input_deps.py', 107, 'test_input_deps_secondary_files'), 'keywords': {'test_input_deps_secondary_files': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00023992099977476755, 'start': 1685951441.571033, 'stop': 1685951441.571274, '$report_type': 'TestReport', 'item_index': 390, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_input_deps.py::test_input_deps_cmdline_opts_relative_deps_cwd + location: ('tests/test_input_deps.py', 73, 'test_input_deps_cmdline_opts_relative_deps_cwd') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_input_deps.py::test_input_deps_secondary_files + location: ('tests/test_input_deps.py', 107, 'test_input_deps_secondary_files') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_basic_pack', 'location': ('tests/test_misc_cli.py', 35, 'test_basic_pack'), 'keywords': {'test_basic_pack': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'")], 'duration': 0.7982027429998197, 'start': 1685951441.066327, 'stop': 1685951441.864511, '$report_type': 'TestReport', 'item_index': 449, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_basic_pack', 'location': ('tests/test_misc_cli.py', 35, 'test_basic_pack'), 'keywords': {'test_basic_pack': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'")], 'duration': 0.00028405200009729015, 'start': 1685951441.865134, 'stop': 1685951441.86542, '$report_type': 'TestReport', 'item_index': 449, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_misc_cli.py::test_basic_pack + location: ('tests/test_misc_cli.py', 35, 'test_basic_pack') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_basic_print_subgraph', 'location': ('tests/test_misc_cli.py', 42, 'test_basic_print_subgraph'), 'keywords': {'test_basic_print_subgraph': 1, 'skipif': 1, 'pytestmark': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002091979995384463, 'start': 1685951441.866752, 'stop': 1685951441.866963, '$report_type': 'TestReport', 'item_index': 450, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_misc_cli.py::test_basic_print_subgraph + location: ('tests/test_misc_cli.py', 42, 'test_basic_print_subgraph') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_workflow', 'location': ('tests/test_loop.py', 59, 'test_validate_loop_fail_on_workflow'), 'keywords': {'test_validate_loop_fail_on_workflow': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-workflow.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-workflow.cwl:13:7: object id 'tests/loop/invalid-loop-workflow.cwl#i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed initialization:\ntests/loop/invalid-loop-workflow.cwl:10:3: Unsupported requirement http://commonwl.org/cwltool#Loop.\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-workflow.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-workflow.cwl:13:7: object id 'tests/loop/invalid-loop-workflow.cwl#i1' previously defined\nERROR cwltool:main.py:1211 Tool definition failed initialization:\ntests/loop/invalid-loop-workflow.cwl:10:3: Unsupported requirement http://commonwl.org/cwltool#Loop.")], 'duration': 0.9319351900003312, 'start': 1685951440.9462762, 'stop': 1685951441.878189, '$report_type': 'TestReport', 'item_index': 423, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_workflow', 'location': 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'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-workflow.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-workflow.cwl:13:7: object id 'tests/loop/invalid-loop-workflow.cwl#i1' previously defined\nERROR cwltool:main.py:1211 Tool definition failed initialization:\ntests/loop/invalid-loop-workflow.cwl:10:3: Unsupported requirement http://commonwl.org/cwltool#Loop.")], 'duration': 0.00021205800021562027, 'start': 1685951441.8786712, 'stop': 1685951441.878884, '$report_type': 'TestReport', 'item_index': 423, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_command_line_tool', 'location': ('tests/test_loop.py', 69, 'test_validate_loop_fail_on_command_line_tool'), 'keywords': {'test_validate_loop_fail_on_command_line_tool': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002561719993536826, 'start': 1685951441.879803, 'stop': 1685951441.8800619, '$report_type': 'TestReport', 'item_index': 424, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_on_workflow + location: ('tests/test_loop.py', 59, 'test_validate_loop_fail_on_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_on_command_line_tool + location: ('tests/test_loop.py', 69, 'test_validate_loop_fail_on_command_line_tool') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_nested_loops', 'location': ('tests/test_loop.py', 223, 'test_nested_loops'), 'keywords': {'test_nested_loops': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/loop-inside-loop.cwl:41:13: object id 'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop.cwl:41:13: object id 'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop.cwl:52:7: object id 'tests/loop/loop-inside-loop.cwl#loop1/i2' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _11] start\n\x1b[1;30mINFO\x1b[0m [workflow _11] starting step loop1\n\x1b[1;30mINFO\x1b[0m [step loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1] starting step loop2\n\x1b[1;30mINFO\x1b[0m [step loop2] start\n\x1b[1;30mINFO\x1b[0m [step loop2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] starting step loop2_2\n\x1b[1;30mINFO\x1b[0m [step loop2_2] start\n\x1b[1;30mINFO\x1b[0m [step loop2_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_2] start\n\x1b[1;30mINFO\x1b[0m [step loop2_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] starting step loop2_3\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _11] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:41:13: object id \'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:41:13: object id \'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:52:7: object id \'tests/loop/loop-inside-loop.cwl#loop1/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step loop1\nDEBUG cwltool:workflow_job.py:727 [step loop1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1] starting step loop2\nDEBUG cwltool:workflow_job.py:727 [step loop2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2] Iteration 1 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 1\nDEBUG cwltool:workflow_job.py:925 [step loop2] inputs was {\n "i1": 2,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step loop2] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1] outputs {\n "o1": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_2] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_2] inputs {\n "i1": 1,\n "i2": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_2] starting step loop2_2\nDEBUG cwltool:workflow_job.py:727 [step loop2_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 2\n}\nINFO cwltool:workflow_job.py:75 [step loop2_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_2] Iteration 2 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_2] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 2\nDEBUG cwltool:workflow_job.py:925 [step loop2_2] inputs was {\n "i1": 3,\n "i2": 2\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:572 [step loop2_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_2] outputs {\n "o1": 3\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_3] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_3] inputs {\n "i1": 1,\n "i2": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_3] starting step loop2_3\nDEBUG cwltool:workflow_job.py:727 [step loop2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 3\n}\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_3] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop2_3] inputs was {\n "i1": 4,\n "i2": 3\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:572 [step loop2_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_3] outputs {\n "o1": 4\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop1] loop condition $(inputs.i2 < 4) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop1] inputs was {\n "i1": 1,\n "i2": 4\n}\nDEBUG cwltool:workflow_job.py:564 [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {\n "o1": [\n 2,\n 3,\n 4\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp86kxxkxs\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpx1mswbm8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpicj1_df4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0soc3lb5\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.053414222000356, 'start': 1685951441.092515, 'stop': 1685951442.145904, '$report_type': 'TestReport', 'item_index': 437, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_nested_loops', 'location': ('tests/test_loop.py', 223, 'test_nested_loops'), 'keywords': {'test_nested_loops': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/loop-inside-loop.cwl:41:13: object id 'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop.cwl:41:13: object id 'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop.cwl:52:7: object id 'tests/loop/loop-inside-loop.cwl#loop1/i2' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _11] start\n\x1b[1;30mINFO\x1b[0m [workflow _11] starting step loop1\n\x1b[1;30mINFO\x1b[0m [step loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1] starting step loop2\n\x1b[1;30mINFO\x1b[0m [step loop2] start\n\x1b[1;30mINFO\x1b[0m [step loop2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] starting step loop2_2\n\x1b[1;30mINFO\x1b[0m [step loop2_2] start\n\x1b[1;30mINFO\x1b[0m [step loop2_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_2] start\n\x1b[1;30mINFO\x1b[0m [step loop2_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] starting step loop2_3\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _11] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:41:13: object id \'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:41:13: object id \'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:52:7: object id \'tests/loop/loop-inside-loop.cwl#loop1/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step loop1\nDEBUG cwltool:workflow_job.py:727 [step loop1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1] starting step loop2\nDEBUG cwltool:workflow_job.py:727 [step loop2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2] Iteration 1 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 1\nDEBUG cwltool:workflow_job.py:925 [step loop2] inputs was {\n "i1": 2,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step loop2] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1] outputs {\n "o1": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_2] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_2] inputs {\n "i1": 1,\n "i2": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_2] starting step loop2_2\nDEBUG cwltool:workflow_job.py:727 [step loop2_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 2\n}\nINFO cwltool:workflow_job.py:75 [step loop2_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_2] Iteration 2 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_2] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 2\nDEBUG cwltool:workflow_job.py:925 [step loop2_2] inputs was {\n "i1": 3,\n "i2": 2\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:572 [step loop2_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_2] outputs {\n "o1": 3\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_3] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_3] inputs {\n "i1": 1,\n "i2": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_3] starting step loop2_3\nDEBUG cwltool:workflow_job.py:727 [step loop2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 3\n}\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_3] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop2_3] inputs was {\n "i1": 4,\n "i2": 3\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:572 [step loop2_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_3] outputs {\n "o1": 4\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop1] loop condition $(inputs.i2 < 4) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop1] inputs was {\n "i1": 1,\n "i2": 4\n}\nDEBUG cwltool:workflow_job.py:564 [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {\n "o1": [\n 2,\n 3,\n 4\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp86kxxkxs\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpx1mswbm8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpicj1_df4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0soc3lb5\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00048784200043883175, 'start': 1685951442.147024, 'stop': 1685951442.147514, '$report_type': 'TestReport', 'item_index': 437, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_nested_loops + location: ('tests/test_loop.py', 223, 'test_nested_loops') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_nested_loops_all + location: ('tests/test_loop.py', 236, 'test_nested_loops_all') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_nested_loops_all', 'location': ('tests/test_loop.py', 236, 'test_nested_loops_all'), 'keywords': {'test_nested_loops_all': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000564637000024959, 'start': 1685951442.149386, 'stop': 1685951442.149954, '$report_type': 'TestReport', 'item_index': 438, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_write_summary', 'location': ('tests/test_examples.py', 1326, 'test_write_summary'), 'keywords': {'test_write_summary': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl",\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:982 [job no-parameters-echo.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job no-parameters-echo.cwl] {\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job no-parameters-echo.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job no-parameters-echo.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n }\n]\nDEBUG cwltool:job.py:215 [job no-parameters-echo.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job no-parameters-echo.cwl] /private/tmp/docker_tmp2imu6nl2$ echo > /private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job no-parameters-echo.cwl] completed success\nDEBUG cwltool:job.py:422 [job no-parameters-echo.cwl] outputs {\n "e_out": {\n "location": "file:///private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "basename": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameroot": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job no-parameters-echo.cwl] Removing input staging directory /private/tmp/docker_tmpxbhyjn_4\nDEBUG cwltool:job.py:454 [job no-parameters-echo.cwl] Removing temporary directory /private/tmp/docker_tmpo4kfuhls\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_write_summary0/out1/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2imu6nl2\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl",\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:982 [job no-parameters-echo.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job no-parameters-echo.cwl_2] {\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job no-parameters-echo.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job no-parameters-echo.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n }\n]\nDEBUG cwltool:job.py:215 [job no-parameters-echo.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job no-parameters-echo.cwl_2] /private/tmp/docker_tmpkot0d5xg$ echo > /private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job no-parameters-echo.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job no-parameters-echo.cwl_2] outputs {\n "e_out": {\n "location": "file:///private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "basename": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameroot": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job no-parameters-echo.cwl_2] Removing input staging directory /private/tmp/docker_tmplio_v9ds\nDEBUG cwltool:job.py:454 [job no-parameters-echo.cwl_2] Removing temporary directory /private/tmp/docker_tmpcl153tce\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_write_summary0/out2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkot0d5xg\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.5343125399995188, 'start': 1685951440.678324, 'stop': 1685951442.2126021, '$report_type': 'TestReport', 'item_index': 304, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_write_summary', 'location': ('tests/test_examples.py', 1326, 'test_write_summary'), 'keywords': {'test_write_summary': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl",\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:982 [job no-parameters-echo.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job no-parameters-echo.cwl] {\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job no-parameters-echo.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job no-parameters-echo.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n }\n]\nDEBUG cwltool:job.py:215 [job no-parameters-echo.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job no-parameters-echo.cwl] /private/tmp/docker_tmp2imu6nl2$ echo > /private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job no-parameters-echo.cwl] completed success\nDEBUG cwltool:job.py:422 [job no-parameters-echo.cwl] outputs {\n "e_out": {\n "location": "file:///private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "basename": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameroot": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job no-parameters-echo.cwl] Removing input staging directory /private/tmp/docker_tmpxbhyjn_4\nDEBUG cwltool:job.py:454 [job no-parameters-echo.cwl] Removing temporary directory /private/tmp/docker_tmpo4kfuhls\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_write_summary0/out1/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2imu6nl2\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl",\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:982 [job no-parameters-echo.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job no-parameters-echo.cwl_2] {\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job no-parameters-echo.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job no-parameters-echo.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n }\n]\nDEBUG cwltool:job.py:215 [job no-parameters-echo.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job no-parameters-echo.cwl_2] /private/tmp/docker_tmpkot0d5xg$ echo > /private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job no-parameters-echo.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job no-parameters-echo.cwl_2] outputs {\n "e_out": {\n "location": "file:///private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "basename": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameroot": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job no-parameters-echo.cwl_2] Removing input staging directory /private/tmp/docker_tmplio_v9ds\nDEBUG cwltool:job.py:454 [job no-parameters-echo.cwl_2] Removing temporary directory /private/tmp/docker_tmpcl153tce\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_write_summary0/out2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkot0d5xg\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007945969991851598, 'start': 1685951442.2140448, 'stop': 1685951442.2148411, '$report_type': 'TestReport', 'item_index': 304, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_write_summary + location: ('tests/test_examples.py', 1326, 'test_write_summary') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_compute_checksum + location: ('tests/test_examples.py', 1355, 'test_compute_checksum') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compute_checksum', 'location': ('tests/test_examples.py', 1355, 'test_compute_checksum'), 'keywords': {'test_compute_checksum': 1, 'skipif': 1, 'pytestmark': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018198719999418245, 'start': 1685951442.217089, 'stop': 1685951442.21891, '$report_type': 'TestReport', 'item_index': 305, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compute_checksum', 'location': ('tests/test_examples.py', 1355, 'test_compute_checksum'), 'keywords': {'test_compute_checksum': 1, 'skipif': 1, 'pytestmark': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\'\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n },\n "reverse": false\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m [job cat-tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z$ cat < /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m [job cat-tool.cwl] completed success\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] outputs {\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/kaqzgbml\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_compute_checksum0/output\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job cat-tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job cat-tool.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n },\n "reverse": false\n}\nDEBUG cwltool:command_line_tool.py:1000 [job cat-tool.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job cat-tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n }\n]\nDEBUG cwltool:job.py:215 [job cat-tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job cat-tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z$ cat < /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job cat-tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job cat-tool.cwl] outputs {\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job cat-tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd\nDEBUG cwltool:job.py:454 [job cat-tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/kaqzgbml\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_compute_checksum0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z')], 'duration': 0.04705045799983054, 'start': 1685951442.219559, 'stop': 1685951442.2666109, '$report_type': 'TestReport', 'item_index': 305, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_compute_checksum', 'location': ('tests/test_examples.py', 1355, 'test_compute_checksum'), 'keywords': {'test_compute_checksum': 1, 'skipif': 1, 'pytestmark': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\'\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n },\n "reverse": false\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m [job cat-tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z$ cat < /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m [job cat-tool.cwl] completed success\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] outputs {\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/kaqzgbml\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_compute_checksum0/output\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job cat-tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job cat-tool.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n },\n "reverse": false\n}\nDEBUG cwltool:command_line_tool.py:1000 [job cat-tool.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job cat-tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n }\n]\nDEBUG cwltool:job.py:215 [job cat-tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job cat-tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z$ cat < /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job cat-tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job cat-tool.cwl] outputs {\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job cat-tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd\nDEBUG cwltool:job.py:454 [job cat-tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/kaqzgbml\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_compute_checksum0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z')], 'duration': 0.0006137840000519645, 'start': 1685951442.267637, 'stop': 1685951442.268252, '$report_type': 'TestReport', 'item_index': 305, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_compute_checksum + location: ('tests/test_examples.py', 1355, 'test_compute_checksum') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::TestMpiRun::test_simple_mpi_tool + location: ('tests/test_mpi.py', 137, 'TestMpiRun.test_simple_mpi_tool') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_tool', 'location': ('tests/test_mpi.py', 137, 'TestMpiRun.test_simple_mpi_tool'), 'keywords': {'test_simple_mpi_tool': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.007654691000425373, 'start': 1685951442.270446, 'stop': 1685951442.278104, '$report_type': 'TestReport', 'item_index': 456, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_secondary_files', 'location': ('tests/test_input_deps.py', 107, 'test_input_deps_secondary_files'), 'keywords': {'test_input_deps_secondary_files': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl'")], 'duration': 0.9784087640000507, 'start': 1685951441.571808, 'stop': 1685951442.550194, '$report_type': 'TestReport', 'item_index': 390, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_secondary_files', 'location': ('tests/test_input_deps.py', 107, 'test_input_deps_secondary_files'), 'keywords': {'test_input_deps_secondary_files': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl'")], 'duration': 0.00031209000007947907, 'start': 1685951442.55082, 'stop': 1685951442.5511339, '$report_type': 'TestReport', 'item_index': 390, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_input_deps.py::test_input_deps_secondary_files + location: ('tests/test_input_deps.py', 107, 'test_input_deps_secondary_files') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_iwdr.py::test_newline_in_entry + location: ('tests/test_iwdr.py', 15, 'test_newline_in_entry') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_newline_in_entry', 'location': ('tests/test_iwdr.py', 15, 'test_newline_in_entry'), 'keywords': {'test_newline_in_entry': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002904470002249582, 'start': 1685951442.552471, 'stop': 1685951442.552763, '$report_type': 'TestReport', 'item_index': 391, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_basic_print_subgraph', 'location': ('tests/test_misc_cli.py', 42, 'test_basic_print_subgraph'), 'keywords': {'test_basic_print_subgraph': 1, 'skipif': 1, 'pytestmark': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines1-wf.cwl'\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.9936495560004914, 'start': 1685951441.867296, 'stop': 1685951442.8609228, '$report_type': 'TestReport', 'item_index': 450, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_basic_print_subgraph', 'location': ('tests/test_misc_cli.py', 42, 'test_basic_print_subgraph'), 'keywords': {'test_basic_print_subgraph': 1, 'skipif': 1, 'pytestmark': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines1-wf.cwl'\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.0003293109994046972, 'start': 1685951442.8618062, 'stop': 1685951442.862138, '$report_type': 'TestReport', 'item_index': 450, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_misc_cli.py::test_basic_print_subgraph + location: ('tests/test_misc_cli.py', 42, 'test_basic_print_subgraph') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_misc_cli.py::test_error_graph_with_no_default + location: ('tests/test_misc_cli.py', 55, 'test_error_graph_with_no_default') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_error_graph_with_no_default', 'location': ('tests/test_misc_cli.py', 55, 'test_error_graph_with_no_default'), 'keywords': {'test_error_graph_with_no_default': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002873619996535126, 'start': 1685951442.863449, 'stop': 1685951442.863738, '$report_type': 'TestReport', 'item_index': 451, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_command_line_tool', 'location': ('tests/test_loop.py', 69, 'test_validate_loop_fail_on_command_line_tool'), 'keywords': {'test_validate_loop_fail_on_command_line_tool': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-command-line-tool.cwl:11:7: object id 'tests/loop/invalid-loop-command-line-tool.cwl#i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed initialization:\ntests/loop/invalid-loop-command-line-tool.cwl:8:3: Unsupported requirement http://commonwl.org/cwltool#Loop.\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-command-line-tool.cwl:11:7: object id 'tests/loop/invalid-loop-command-line-tool.cwl#i1' previously defined\nERROR cwltool:main.py:1211 Tool definition failed initialization:\ntests/loop/invalid-loop-command-line-tool.cwl:8:3: Unsupported requirement http://commonwl.org/cwltool#Loop.")], 'duration': 1.063583369999833, 'start': 1685951441.880509, 'stop': 1685951442.9440682, '$report_type': 'TestReport', 'item_index': 424, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_command_line_tool', 'location': ('tests/test_loop.py', 69, 'test_validate_loop_fail_on_command_line_tool'), 'keywords': {'test_validate_loop_fail_on_command_line_tool': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-command-line-tool.cwl:11:7: object id 'tests/loop/invalid-loop-command-line-tool.cwl#i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed initialization:\ntests/loop/invalid-loop-command-line-tool.cwl:8:3: Unsupported requirement http://commonwl.org/cwltool#Loop.\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-command-line-tool.cwl:11:7: object id 'tests/loop/invalid-loop-command-line-tool.cwl#i1' previously defined\nERROR cwltool:main.py:1211 Tool definition failed initialization:\ntests/loop/invalid-loop-command-line-tool.cwl:8:3: Unsupported requirement http://commonwl.org/cwltool#Loop.")], 'duration': 0.0002101680001942441, 'start': 1685951442.944543, 'stop': 1685951442.944754, '$report_type': 'TestReport', 'item_index': 424, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_expression_tool', 'location': ('tests/test_loop.py', 79, 'test_validate_loop_fail_on_expression_tool'), 'keywords': {'test_validate_loop_fail_on_expression_tool': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00019860999964294024, 'start': 1685951442.945764, 'stop': 1685951442.945964, '$report_type': 'TestReport', 'item_index': 425, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_on_command_line_tool + location: ('tests/test_loop.py', 69, 'test_validate_loop_fail_on_command_line_tool') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_on_expression_tool + location: ('tests/test_loop.py', 79, 'test_validate_loop_fail_on_expression_tool') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_file_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 155, 'test_disable_file_creation_in_outdir_with_ext'), 'keywords': {'test_disable_file_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmpxknywf47/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "path": "/private/tmp/docker_tmpxknywf47/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl'\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] /private/tmp/docker_tmpxknywf47$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpxknywf47,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp9frq7sxn,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpjuxvtp7d/20230605095042-024812.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl",\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value"\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updateval_inplace.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updateval_inplace.cwl] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "size": 102,\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updateval_inplace.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updateval_inplace.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job updateval_inplace.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updateval_inplace.cwl] /private/tmp/docker_tmpxknywf47$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpxknywf47,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp9frq7sxn,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpjuxvtp7d/20230605095042-024812.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py \\\n value\nINFO cwltool:job.py:905 [job updateval_inplace.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job updateval_inplace.cwl] completed success\nDEBUG cwltool:job.py:422 [job updateval_inplace.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxknywf47/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job updateval_inplace.cwl] Removing input staging directory /private/tmp/docker_tmpju1om5_7\nDEBUG cwltool:job.py:454 [job updateval_inplace.cwl] Removing temporary directory /private/tmp/docker_tmp9frq7sxn\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxknywf47\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.8482773919995452, 'start': 1685951441.2034738, 'stop': 1685951443.0517068, '$report_type': 'TestReport', 'item_index': 372, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_file_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 155, 'test_disable_file_creation_in_outdir_with_ext'), 'keywords': {'test_disable_file_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmpxknywf47/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "path": "/private/tmp/docker_tmpxknywf47/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl'\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] /private/tmp/docker_tmpxknywf47$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpxknywf47,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp9frq7sxn,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpjuxvtp7d/20230605095042-024812.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl",\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value"\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updateval_inplace.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updateval_inplace.cwl] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "size": 102,\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updateval_inplace.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updateval_inplace.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job updateval_inplace.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updateval_inplace.cwl] /private/tmp/docker_tmpxknywf47$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpxknywf47,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp9frq7sxn,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpjuxvtp7d/20230605095042-024812.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py \\\n value\nINFO cwltool:job.py:905 [job updateval_inplace.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job updateval_inplace.cwl] completed success\nDEBUG cwltool:job.py:422 [job updateval_inplace.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxknywf47/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job updateval_inplace.cwl] Removing input staging directory /private/tmp/docker_tmpju1om5_7\nDEBUG cwltool:job.py:454 [job updateval_inplace.cwl] Removing temporary directory /private/tmp/docker_tmp9frq7sxn\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxknywf47\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008131670001603197, 'start': 1685951443.053161, 'stop': 1685951443.053976, '$report_type': 'TestReport', 'item_index': 372, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_disable_file_creation_in_outdir_with_ext + location: ('tests/test_ext.py', 155, 'test_disable_file_creation_in_outdir_with_ext') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_ext.py::test_disable_dir_creation_in_outdir_with_ext + location: ('tests/test_ext.py', 186, 'test_disable_dir_creation_in_outdir_with_ext') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_dir_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 186, 'test_disable_dir_creation_in_outdir_with_ext'), 'keywords': {'test_disable_dir_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0028105779992984026, 'start': 1685951443.0566452, 'stop': 1685951443.059459, '$report_type': 'TestReport', 'item_index': 373, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_nested_loops_all', 'location': ('tests/test_loop.py', 236, 'test_nested_loops_all'), 'keywords': {'test_nested_loops_all': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/loop-inside-loop-all.cwl:45:13: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop-all.cwl:45:13: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop-all.cwl:56:7: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/i2' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _12] start\n\x1b[1;30mINFO\x1b[0m [workflow _12] starting step loop1_2\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] starting step loop2_4\n\x1b[1;30mINFO\x1b[0m [step loop2_4] start\n\x1b[1;30mINFO\x1b[0m [step loop2_4] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] starting step loop2_5\n\x1b[1;30mINFO\x1b[0m [step loop2_5] start\n\x1b[1;30mINFO\x1b[0m [step loop2_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_5] start\n\x1b[1;30mINFO\x1b[0m [step loop2_5] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] starting step loop2_6\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _12] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:45:13: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:45:13: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:56:7: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step loop1_2\nDEBUG cwltool:workflow_job.py:727 [step loop1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_4] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_4] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_4] starting step loop2_4\nDEBUG cwltool:workflow_job.py:727 [step loop2_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop2_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_4] Iteration 1 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_4] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 1\nDEBUG cwltool:workflow_job.py:925 [step loop2_4] inputs was {\n "i1": 2,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_4] outputs {\n "o1": [\n 2\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_5] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_5] inputs {\n "i1": 1,\n "i2": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_5] starting step loop2_5\nDEBUG cwltool:workflow_job.py:727 [step loop2_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 2\n}\nINFO cwltool:workflow_job.py:75 [step loop2_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_5] Iteration 2 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_5] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 2\nDEBUG cwltool:workflow_job.py:925 [step loop2_5] inputs was {\n "i1": 3,\n "i2": 2\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2,\n 3\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_5] outputs {\n "o1": [\n 2,\n 3\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2,\n 3\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_6] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_6] inputs {\n "i1": 1,\n "i2": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_6] starting step loop2_6\nDEBUG cwltool:workflow_job.py:727 [step loop2_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 3\n}\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_6] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop2_6] inputs was {\n "i1": 4,\n "i2": 3\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_6] outputs {\n "o1": [\n 2,\n 3,\n 4\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop1_2] loop condition $(inputs.i2 < 4) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop1_2] inputs was {\n "i1": 1,\n "i2": 4\n}\nDEBUG cwltool:workflow_job.py:564 [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n [\n 2\n ],\n [\n 2,\n 3\n ],\n [\n 2,\n 3,\n 4\n ]\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {\n "o1": [\n [\n 2\n ],\n [\n 2,\n 3\n ],\n [\n 2,\n 3,\n 4\n ]\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpns729pai\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwax8eltf\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp96zdj6k5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_ukam9wx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1771456070000568, 'start': 1685951442.150581, 'stop': 1685951443.327698, '$report_type': 'TestReport', 'item_index': 438, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_nested_loops_all', 'location': ('tests/test_loop.py', 236, 'test_nested_loops_all'), 'keywords': {'test_nested_loops_all': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/loop-inside-loop-all.cwl:45:13: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop-all.cwl:45:13: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop-all.cwl:56:7: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/i2' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _12] start\n\x1b[1;30mINFO\x1b[0m [workflow _12] starting step loop1_2\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] starting step loop2_4\n\x1b[1;30mINFO\x1b[0m [step loop2_4] start\n\x1b[1;30mINFO\x1b[0m [step loop2_4] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] starting step loop2_5\n\x1b[1;30mINFO\x1b[0m [step loop2_5] start\n\x1b[1;30mINFO\x1b[0m [step loop2_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_5] start\n\x1b[1;30mINFO\x1b[0m [step loop2_5] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] starting step loop2_6\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _12] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:45:13: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:45:13: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:56:7: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step loop1_2\nDEBUG cwltool:workflow_job.py:727 [step loop1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_4] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_4] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_4] starting step loop2_4\nDEBUG cwltool:workflow_job.py:727 [step loop2_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop2_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_4] Iteration 1 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_4] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 1\nDEBUG cwltool:workflow_job.py:925 [step loop2_4] inputs was {\n "i1": 2,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_4] outputs {\n "o1": [\n 2\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_5] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_5] inputs {\n "i1": 1,\n "i2": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_5] starting step loop2_5\nDEBUG cwltool:workflow_job.py:727 [step loop2_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 2\n}\nINFO cwltool:workflow_job.py:75 [step loop2_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_5] Iteration 2 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_5] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 2\nDEBUG cwltool:workflow_job.py:925 [step loop2_5] inputs was {\n "i1": 3,\n "i2": 2\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2,\n 3\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_5] outputs {\n "o1": [\n 2,\n 3\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2,\n 3\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_6] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_6] inputs {\n "i1": 1,\n "i2": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_6] starting step loop2_6\nDEBUG cwltool:workflow_job.py:727 [step loop2_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 3\n}\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_6] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop2_6] inputs was {\n "i1": 4,\n "i2": 3\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_6] outputs {\n "o1": [\n 2,\n 3,\n 4\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop1_2] loop condition $(inputs.i2 < 4) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop1_2] inputs was {\n "i1": 1,\n "i2": 4\n}\nDEBUG cwltool:workflow_job.py:564 [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n [\n 2\n ],\n [\n 2,\n 3\n ],\n [\n 2,\n 3,\n 4\n ]\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {\n "o1": [\n [\n 2\n ],\n [\n 2,\n 3\n ],\n [\n 2,\n 3,\n 4\n ]\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpns729pai\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwax8eltf\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp96zdj6k5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_ukam9wx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00034923299972433597, 'start': 1685951443.328602, 'stop': 1685951443.328952, '$report_type': 'TestReport', 'item_index': 438, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_nested_loops_all + location: ('tests/test_loop.py', 236, 'test_nested_loops_all') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_multi_source_loop_input + location: ('tests/test_loop.py', 249, 'test_multi_source_loop_input') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input', 'location': ('tests/test_loop.py', 249, 'test_multi_source_loop_input'), 'keywords': {'test_multi_source_loop_input': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00032360799923480954, 'start': 1685951443.331817, 'stop': 1685951443.332142, '$report_type': 'TestReport', 'item_index': 439, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_newline_in_entry', 'location': ('tests/test_iwdr.py', 15, 'test_newline_in_entry'), 'keywords': {'test_newline_in_entry': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] {\n "message": "hello"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] initial work dir {\n "_:2a0436b5-e8e0-4317-9dff-723871e47051": [\n "CONFIGVAR=hello\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn/example.conf",\n "CreateFile",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mINFO\x1b[0m [job iwdr-entry.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn$ cat \\\n example.conf\nCONFIGVAR=hello\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mINFO\x1b[0m [job iwdr-entry.cwl] completed success\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] outputs {\n "out": "CONFIGVAR=hello\\n"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9_gw9k9h\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/bwdf_fga\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr-entry.cwl] initial work dir {\n "_:2a0436b5-e8e0-4317-9dff-723871e47051": [\n "CONFIGVAR=hello\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr-entry.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn$ cat \\\n example.conf\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr-entry.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr-entry.cwl] outputs {\n "out": "CONFIGVAR=hello\\n"\n}\nDEBUG cwltool:job.py:446 [job iwdr-entry.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9_gw9k9h\nDEBUG cwltool:job.py:454 [job iwdr-entry.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/bwdf_fga\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn')], 'duration': 0.8588610730002983, 'start': 1685951442.5531578, 'stop': 1685951443.411999, '$report_type': 'TestReport', 'item_index': 391, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_newline_in_entry', 'location': ('tests/test_iwdr.py', 15, 'test_newline_in_entry'), 'keywords': {'test_newline_in_entry': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] {\n "message": "hello"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] initial work dir {\n "_:2a0436b5-e8e0-4317-9dff-723871e47051": [\n "CONFIGVAR=hello\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn/example.conf",\n "CreateFile",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mINFO\x1b[0m [job iwdr-entry.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn$ cat \\\n example.conf\nCONFIGVAR=hello\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mINFO\x1b[0m [job iwdr-entry.cwl] completed success\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] outputs {\n "out": "CONFIGVAR=hello\\n"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9_gw9k9h\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/bwdf_fga\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr-entry.cwl] initial work dir {\n "_:2a0436b5-e8e0-4317-9dff-723871e47051": [\n "CONFIGVAR=hello\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr-entry.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn$ cat \\\n example.conf\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr-entry.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr-entry.cwl] outputs {\n "out": "CONFIGVAR=hello\\n"\n}\nDEBUG cwltool:job.py:446 [job iwdr-entry.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9_gw9k9h\nDEBUG cwltool:job.py:454 [job iwdr-entry.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/bwdf_fga\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn')], 'duration': 0.0004247679999025422, 'start': 1685951443.413008, 'stop': 1685951443.413434, '$report_type': 'TestReport', 'item_index': 391, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_iwdr.py::test_newline_in_entry + location: ('tests/test_iwdr.py', 15, 'test_newline_in_entry') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_iwdr.py::test_empty_file_creation + location: ('tests/test_iwdr.py', 22, 'test_empty_file_creation') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_empty_file_creation', 'location': ('tests/test_iwdr.py', 22, 'test_empty_file_creation'), 'keywords': {'test_empty_file_creation': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002311670004928601, 'start': 1685951443.4147048, 'stop': 1685951443.414937, '$report_type': 'TestReport', 'item_index': 392, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_tool', 'location': ('tests/test_mpi.py', 137, 'TestMpiRun.test_simple_mpi_tool'), 'keywords': {'test_simple_mpi_tool': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job mpi_simple.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_simple.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_simple.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_simple.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_simple.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_simple.cwl] /private/tmp/docker_tmpsrrf7xpl$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 2 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_simple.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_simple.cwl] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798",\n "basename": "412772b89f251957f4c82220883acbf443033798",\n "nameroot": "412772b89f251957f4c82220883acbf443033798",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$16cc94e5a27d65270f541b21404ad3b89fab0ddf",\n "size": 12,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_simple.cwl] Removing input staging directory /private/tmp/docker_tmpsl_eahho\nDEBUG cwltool:job.py:454 [job mpi_simple.cwl] Removing temporary directory /private/tmp/docker_tmphv_v29r_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_simple_mpi_tool0/412772b89f251957f4c82220883acbf443033798\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsrrf7xpl\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.2947465670004021, 'start': 1685951442.2788281, 'stop': 1685951443.573545, '$report_type': 'TestReport', 'item_index': 456, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_tool', 'location': ('tests/test_mpi.py', 137, 'TestMpiRun.test_simple_mpi_tool'), 'keywords': {'test_simple_mpi_tool': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job mpi_simple.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_simple.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_simple.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_simple.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_simple.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_simple.cwl] /private/tmp/docker_tmpsrrf7xpl$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 2 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_simple.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_simple.cwl] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798",\n "basename": "412772b89f251957f4c82220883acbf443033798",\n "nameroot": "412772b89f251957f4c82220883acbf443033798",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$16cc94e5a27d65270f541b21404ad3b89fab0ddf",\n "size": 12,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_simple.cwl] Removing input staging directory /private/tmp/docker_tmpsl_eahho\nDEBUG cwltool:job.py:454 [job mpi_simple.cwl] Removing temporary directory /private/tmp/docker_tmphv_v29r_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_simple_mpi_tool0/412772b89f251957f4c82220883acbf443033798\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsrrf7xpl\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000572511999962444, 'start': 1685951443.5744262, 'stop': 1685951443.575, '$report_type': 'TestReport', 'item_index': 456, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::TestMpiRun::test_simple_mpi_tool + location: ('tests/test_mpi.py', 137, 'TestMpiRun.test_simple_mpi_tool') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::TestMpiRun::test_simple_mpi_nproc_expr + location: ('tests/test_mpi.py', 154, 'TestMpiRun.test_simple_mpi_nproc_expr') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_nproc_expr', 'location': ('tests/test_mpi.py', 154, 'TestMpiRun.test_simple_mpi_nproc_expr'), 'keywords': {'test_simple_mpi_nproc_expr': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016168849997484358, 'start': 1685951443.576514, 'stop': 1685951443.578132, '$report_type': 'TestReport', 'item_index': 457, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_error_graph_with_no_default', 'location': ('tests/test_misc_cli.py', 55, 'test_error_graph_with_no_default'), 'keywords': {'test_error_graph_with_no_default': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl'\nERROR cwltool:main.py:1211 Tool definition failed initialization:\nTool file contains graph of multiple objects, must specify one of #echo, #cat, #collision")], 'duration': 0.9360590020005475, 'start': 1685951442.8640919, 'stop': 1685951443.800129, '$report_type': 'TestReport', 'item_index': 451, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_error_graph_with_no_default', 'location': ('tests/test_misc_cli.py', 55, 'test_error_graph_with_no_default'), 'keywords': {'test_error_graph_with_no_default': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl'\nERROR cwltool:main.py:1211 Tool definition failed initialization:\nTool file contains graph of multiple objects, must specify one of #echo, #cat, #collision")], 'duration': 0.00019843600057356525, 'start': 1685951443.800568, 'stop': 1685951443.800767, '$report_type': 'TestReport', 'item_index': 451, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_misc_cli.py::test_error_graph_with_no_default + location: ('tests/test_misc_cli.py', 55, 'test_error_graph_with_no_default') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_misc_cli.py::test_skip_schemas_external_step + location: ('tests/test_misc_cli.py', 67, 'test_skip_schemas_external_step') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_skip_schemas_external_step', 'location': ('tests/test_misc_cli.py', 67, 'test_skip_schemas_external_step'), 'keywords': {'test_skip_schemas_external_step': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00022477499987871852, 'start': 1685951443.801759, 'stop': 1685951443.801984, '$report_type': 'TestReport', 'item_index': 452, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]'), 'keywords': {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_11\nDEBUG cwltool:workflow_job.py:727 [step task2_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_11\nDEBUG cwltool:command_line_tool.py:988 [job task2_9] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_9), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_11\nDEBUG cwltool:workflow_job.py:727 [step task1_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_11\nDEBUG cwltool:command_line_tool.py:988 [job task1_9] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_9] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_9), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task1_9] initial work dir {}\nINFO cwltool:job.py:266 [job task2_9] /private/tmp/docker_tmp6w_kuuwk$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp6w_kuuwk,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpimrbltf0,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-808365.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:266 [job task1_9] /private/tmp/docker_tmpqm8yecor$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqm8yecor,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpxft5vpeu,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-828561.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task2_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_9] completed success\nDEBUG cwltool:job.py:422 [job task2_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6w_kuuwk/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_11] completed success\nDEBUG cwltool:job.py:446 [job task2_9] Removing input staging directory /private/tmp/docker_tmpr2euvrmb\nDEBUG cwltool:job.py:454 [job task2_9] Removing temporary directory /private/tmp/docker_tmpimrbltf0\nINFO cwltool:job.py:905 [job task1_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_9] completed success\nDEBUG cwltool:job.py:422 [job task1_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqm8yecor/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_11] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_9] Removing input staging directory /private/tmp/docker_tmpfumwmmb0\nDEBUG cwltool:job.py:454 [job task1_9] Removing temporary directory /private/tmp/docker_tmpxft5vpeu\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqm8yecor\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp91c3ruq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6w_kuuwk\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.689709309999671, 'start': 1685951441.163031, 'stop': 1685951443.852674, '$report_type': 'TestReport', 'item_index': 277, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]'), 'keywords': {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_11\nDEBUG cwltool:workflow_job.py:727 [step task2_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_11\nDEBUG cwltool:command_line_tool.py:988 [job task2_9] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_9), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_11\nDEBUG cwltool:workflow_job.py:727 [step task1_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_11\nDEBUG cwltool:command_line_tool.py:988 [job task1_9] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_9] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_9), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task1_9] initial work dir {}\nINFO cwltool:job.py:266 [job task2_9] /private/tmp/docker_tmp6w_kuuwk$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp6w_kuuwk,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpimrbltf0,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-808365.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:266 [job task1_9] /private/tmp/docker_tmpqm8yecor$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqm8yecor,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpxft5vpeu,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-828561.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task2_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_9] completed success\nDEBUG cwltool:job.py:422 [job task2_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6w_kuuwk/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_11] completed success\nDEBUG cwltool:job.py:446 [job task2_9] Removing input staging directory /private/tmp/docker_tmpr2euvrmb\nDEBUG cwltool:job.py:454 [job task2_9] Removing temporary directory /private/tmp/docker_tmpimrbltf0\nINFO cwltool:job.py:905 [job task1_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_9] completed success\nDEBUG cwltool:job.py:422 [job task1_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqm8yecor/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_11] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_9] Removing input staging directory /private/tmp/docker_tmpfumwmmb0\nDEBUG cwltool:job.py:454 [job task1_9] Removing temporary directory /private/tmp/docker_tmpxft5vpeu\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqm8yecor\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp91c3ruq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6w_kuuwk\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007029949993011542, 'start': 1685951443.85393, 'stop': 1685951443.854634, '$report_type': 'TestReport', 'item_index': 277, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]'), 'keywords': {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0021138760002941126, 'start': 1685951443.8562508, 'stop': 1685951443.858367, '$report_type': 'TestReport', 'item_index': 278, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_expression_tool', 'location': ('tests/test_loop.py', 79, 'test_validate_loop_fail_on_expression_tool'), 'keywords': {'test_validate_loop_fail_on_expression_tool': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-expression-tool.cwl:11:7: object id 'tests/loop/invalid-loop-expression-tool.cwl#i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-expression-tool.cwl:16:1: checking field 'outputs'\ntests/loop/invalid-loop-expression-tool.cwl:17:3: checking object\n 'tests/loop/invalid-loop-expression-tool.cwl#o1'\ntests/loop/invalid-loop-expression-tool.cwl:19:5: Field 'outputSource' references unknown\n identifier 'subworkflow/o1', tried\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#o1/subworkflow/o1\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#subworkflow/o1\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-expression-tool.cwl:11:7: object id 'tests/loop/invalid-loop-expression-tool.cwl#i1' previously defined\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-expression-tool.cwl:16:1: checking field 'outputs'\ntests/loop/invalid-loop-expression-tool.cwl:17:3: checking object\n 'tests/loop/invalid-loop-expression-tool.cwl#o1'\ntests/loop/invalid-loop-expression-tool.cwl:19:5: Field 'outputSource' references unknown\n identifier 'subworkflow/o1', tried\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#o1/subworkflow/o1\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#subworkflow/o1")], 'duration': 0.9815994860000501, 'start': 1685951442.9462872, 'stop': 1685951443.9278631, '$report_type': 'TestReport', 'item_index': 425, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_expression_tool', 'location': ('tests/test_loop.py', 79, 'test_validate_loop_fail_on_expression_tool'), 'keywords': {'test_validate_loop_fail_on_expression_tool': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-expression-tool.cwl:11:7: object id 'tests/loop/invalid-loop-expression-tool.cwl#i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-expression-tool.cwl:16:1: checking field 'outputs'\ntests/loop/invalid-loop-expression-tool.cwl:17:3: checking object\n 'tests/loop/invalid-loop-expression-tool.cwl#o1'\ntests/loop/invalid-loop-expression-tool.cwl:19:5: Field 'outputSource' references unknown\n identifier 'subworkflow/o1', tried\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#o1/subworkflow/o1\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#subworkflow/o1\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-expression-tool.cwl:11:7: object id 'tests/loop/invalid-loop-expression-tool.cwl#i1' previously defined\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-expression-tool.cwl:16:1: checking field 'outputs'\ntests/loop/invalid-loop-expression-tool.cwl:17:3: checking object\n 'tests/loop/invalid-loop-expression-tool.cwl#o1'\ntests/loop/invalid-loop-expression-tool.cwl:19:5: Field 'outputSource' references unknown\n identifier 'subworkflow/o1', tried\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#o1/subworkflow/o1\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#subworkflow/o1")], 'duration': 0.00020623100044758758, 'start': 1685951443.928481, 'stop': 1685951443.928688, '$report_type': 'TestReport', 'item_index': 425, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_hint', 'location': ('tests/test_loop.py', 89, 'test_validate_loop_fail_on_hint'), 'keywords': {'test_validate_loop_fail_on_hint': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00033236099989153445, 'start': 1685951443.9295738, 'stop': 1685951443.929908, '$report_type': 'TestReport', 'item_index': 426, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_on_expression_tool + location: ('tests/test_loop.py', 79, 'test_validate_loop_fail_on_expression_tool') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_on_hint + location: ('tests/test_loop.py', 89, 'test_validate_loop_fail_on_hint') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_dir_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 186, 'test_disable_dir_creation_in_outdir_with_ext'), 'keywords': {'test_disable_dir_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp",\n "basename": "inp",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp/blurb",\n "basename": "blurb",\n "path": "/private/tmp/docker_tmp9wjf3kni/inp/blurb"\n }\n ],\n "path": "/private/tmp/docker_tmp9wjf3kni/inp"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl'\n\x1b[1;30mINFO\x1b[0m [job updatedir_inplace.cwl] /private/tmp/docker_tmp9wjf3kni$ touch \\\n inp/blurb\n\x1b[1;30mINFO\x1b[0m [job updatedir_inplace.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl",\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updatedir_inplace.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updatedir_inplace.cwl] {\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "basename": "tmp",\n "listing": []\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updatedir_inplace.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "/private/tmp/docker_tmp9wjf3kni/inp",\n "WritableDirectory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updatedir_inplace.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp/blurb"\n }\n]\nDEBUG cwltool:job.py:215 [job updatedir_inplace.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "/private/tmp/docker_tmp9wjf3kni/inp",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updatedir_inplace.cwl] /private/tmp/docker_tmp9wjf3kni$ touch \\\n inp/blurb\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job updatedir_inplace.cwl] completed success\nDEBUG cwltool:job.py:422 [job updatedir_inplace.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp",\n "basename": "inp",\n "nameroot": "inp",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job updatedir_inplace.cwl] Removing input staging directory /private/tmp/docker_tmpg_pphm3n\nDEBUG cwltool:job.py:454 [job updatedir_inplace.cwl] Removing temporary directory /private/tmp/docker_tmps3ugovj7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9wjf3kni\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9035728740000195, 'start': 1685951443.060123, 'stop': 1685951443.963676, '$report_type': 'TestReport', 'item_index': 373, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_disable_dir_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 186, 'test_disable_dir_creation_in_outdir_with_ext'), 'keywords': {'test_disable_dir_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp",\n "basename": "inp",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp/blurb",\n "basename": "blurb",\n "path": "/private/tmp/docker_tmp9wjf3kni/inp/blurb"\n }\n ],\n "path": "/private/tmp/docker_tmp9wjf3kni/inp"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl'\n\x1b[1;30mINFO\x1b[0m [job updatedir_inplace.cwl] /private/tmp/docker_tmp9wjf3kni$ touch \\\n inp/blurb\n\x1b[1;30mINFO\x1b[0m [job updatedir_inplace.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl",\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updatedir_inplace.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updatedir_inplace.cwl] {\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "basename": "tmp",\n "listing": []\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updatedir_inplace.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "/private/tmp/docker_tmp9wjf3kni/inp",\n "WritableDirectory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updatedir_inplace.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp/blurb"\n }\n]\nDEBUG cwltool:job.py:215 [job updatedir_inplace.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "/private/tmp/docker_tmp9wjf3kni/inp",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updatedir_inplace.cwl] /private/tmp/docker_tmp9wjf3kni$ touch \\\n inp/blurb\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job updatedir_inplace.cwl] completed success\nDEBUG cwltool:job.py:422 [job updatedir_inplace.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp",\n "basename": "inp",\n "nameroot": "inp",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job updatedir_inplace.cwl] Removing input staging directory /private/tmp/docker_tmpg_pphm3n\nDEBUG cwltool:job.py:454 [job updatedir_inplace.cwl] Removing temporary directory /private/tmp/docker_tmps3ugovj7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9wjf3kni\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0004848630005653831, 'start': 1685951443.964662, 'stop': 1685951443.965148, '$report_type': 'TestReport', 'item_index': 373, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_disable_dir_creation_in_outdir_with_ext + location: ('tests/test_ext.py', 186, 'test_disable_dir_creation_in_outdir_with_ext') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_ext.py::test_write_write_conflict + location: ('tests/test_ext.py', 207, 'test_write_write_conflict') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_write_write_conflict', 'location': ('tests/test_ext.py', 207, 'test_write_write_conflict'), 'keywords': {'test_write_write_conflict': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012940050000906922, 'start': 1685951443.9662888, 'stop': 1685951443.967584, '$report_type': 'TestReport', 'item_index': 374, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_empty_file_creation', 'location': ('tests/test_iwdr.py', 22, 'test_empty_file_creation'), 'keywords': {'test_empty_file_creation': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-empty.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-empty.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-empty.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-empty.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "empty_file"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr-empty.cwl] initial work dir {\n "_:4fafb878-bba4-4c1b-8b10-31e9ea2e72c1": [\n "",\n "/private/tmp/docker_tmpdtxp2fa3/empty_file",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr-empty.cwl] /private/tmp/docker_tmpdtxp2fa3$ cat \\\n empty_file\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr-empty.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr-empty.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr-empty.cwl] Removing input staging directory /private/tmp/docker_tmpnky3nerk\nDEBUG cwltool:job.py:454 [job iwdr-empty.cwl] Removing temporary directory /private/tmp/docker_tmpwhfbqro0\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdtxp2fa3\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7176641799997014, 'start': 1685951443.415307, 'stop': 1685951444.1329558, '$report_type': 'TestReport', 'item_index': 392, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_empty_file_creation', 'location': ('tests/test_iwdr.py', 22, 'test_empty_file_creation'), 'keywords': {'test_empty_file_creation': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-empty.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-empty.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-empty.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-empty.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "empty_file"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr-empty.cwl] initial work dir {\n "_:4fafb878-bba4-4c1b-8b10-31e9ea2e72c1": [\n "",\n "/private/tmp/docker_tmpdtxp2fa3/empty_file",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr-empty.cwl] /private/tmp/docker_tmpdtxp2fa3$ cat \\\n empty_file\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr-empty.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr-empty.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr-empty.cwl] Removing input staging directory /private/tmp/docker_tmpnky3nerk\nDEBUG cwltool:job.py:454 [job iwdr-empty.cwl] Removing temporary directory /private/tmp/docker_tmpwhfbqro0\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdtxp2fa3\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0004950769998686155, 'start': 1685951444.133989, 'stop': 1685951444.134485, '$report_type': 'TestReport', 'item_index': 392, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_iwdr.py::test_empty_file_creation + location: ('tests/test_iwdr.py', 22, 'test_empty_file_creation') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_iwdr.py::test_passthrough_successive + location: ('tests/test_iwdr.py', 29, 'test_passthrough_successive') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_passthrough_successive', 'location': ('tests/test_iwdr.py', 29, 'test_passthrough_successive'), 'keywords': {'test_passthrough_successive': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018658310000319034, 'start': 1685951444.136501, 'stop': 1685951444.138368, '$report_type': 'TestReport', 'item_index': 393, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input', 'location': ('tests/test_loop.py', 249, 'test_multi_source_loop_input'), 'keywords': {'test_multi_source_loop_input': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/multi-source-loop.cwl:60:7: object id \'tests/loop/multi-source-loop.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/multi-source-loop.cwl:61:11: Source \'osmall\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\ntests/loop/multi-source-loop.cwl:61:19: Source \'obig\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _13] start\n\x1b[1;30mINFO\x1b[0m [workflow _13] starting step loop\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step small_values\n\x1b[1;30mINFO\x1b[0m [step small_values] start\n\x1b[1;30mINFO\x1b[0m [step small_values] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step big_values\n\x1b[1;30mINFO\x1b[0m [step big_values] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step small_values_2\n\x1b[1;30mINFO\x1b[0m [step small_values_2] start\n\x1b[1;30mINFO\x1b[0m [step small_values_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step big_values_2\n\x1b[1;30mINFO\x1b[0m [step big_values_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step small_values_3\n\x1b[1;30mINFO\x1b[0m [step small_values_3] start\n\x1b[1;30mINFO\x1b[0m [step small_values_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step big_values_3\n\x1b[1;30mINFO\x1b[0m [step big_values_3] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_3] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step small_values_4\n\x1b[1;30mINFO\x1b[0m [step small_values_4] start\n\x1b[1;30mINFO\x1b[0m [step small_values_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step big_values_4\n\x1b[1;30mINFO\x1b[0m [step big_values_4] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_4] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step small_values_5\n\x1b[1;30mINFO\x1b[0m [step small_values_5] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_5] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step big_values_5\n\x1b[1;30mINFO\x1b[0m [step big_values_5] start\n\x1b[1;30mINFO\x1b[0m [step big_values_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step small_values_6\n\x1b[1;30mINFO\x1b[0m [step small_values_6] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_6] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step big_values_6\n\x1b[1;30mINFO\x1b[0m [step big_values_6] start\n\x1b[1;30mINFO\x1b[0m [step big_values_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step small_values_7\n\x1b[1;30mINFO\x1b[0m [step small_values_7] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_7] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step big_values_7\n\x1b[1;30mINFO\x1b[0m [step big_values_7] start\n\x1b[1;30mINFO\x1b[0m [step big_values_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] starting step small_values_8\n\x1b[1;30mINFO\x1b[0m [step small_values_8] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_8] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] starting step big_values_8\n\x1b[1;30mINFO\x1b[0m [step big_values_8] start\n\x1b[1;30mINFO\x1b[0m [step big_values_8] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] starting step small_values_9\n\x1b[1;30mINFO\x1b[0m [step small_values_9] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_9] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] starting step big_values_9\n\x1b[1;30mINFO\x1b[0m [step big_values_9] start\n\x1b[1;30mINFO\x1b[0m [step big_values_9] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _13] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/multi-source-loop.cwl:60:7: object id \'tests/loop/multi-source-loop.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/multi-source-loop.cwl:61:11: Source \'osmall\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\ntests/loop/multi-source-loop.cwl:61:19: Source \'obig\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step loop\nDEBUG cwltool:workflow_job.py:727 [step loop] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step small_values\nDEBUG cwltool:workflow_job.py:727 [step small_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step small_values] start\nDEBUG cwltool:workflow_job.py:564 [step small_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step small_values] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step big_values\nDEBUG cwltool:workflow_job.py:727 [step big_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop] outputs {\n "obig": null,\n "osmall": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_2] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_2] inputs {\n "i1": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step small_values_2\nDEBUG cwltool:workflow_job.py:727 [step small_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 2\n}\nINFO cwltool:workflow_job.py:75 [step small_values_2] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 3\n}\nINFO cwltool:workflow_job.py:572 [step small_values_2] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step big_values_2\nDEBUG cwltool:workflow_job.py:727 [step big_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 2\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_2] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_2] inputs was {\n "i1": 2\n}\nINFO cwltool:workflow_job.py:744 [step big_values_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_2] outputs {\n "obig": null,\n "osmall": 3\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_3] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_3] inputs {\n "i1": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step small_values_3\nDEBUG cwltool:workflow_job.py:727 [step small_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 3\n}\nINFO cwltool:workflow_job.py:75 [step small_values_3] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 4\n}\nINFO cwltool:workflow_job.py:572 [step small_values_3] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step big_values_3\nDEBUG cwltool:workflow_job.py:727 [step big_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 3\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_3] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_3] inputs was {\n "i1": 3\n}\nINFO cwltool:workflow_job.py:744 [step big_values_3] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_3] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_3] outputs {\n "obig": null,\n "osmall": 4\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_4] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_4] inputs {\n "i1": 4\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step small_values_4\nDEBUG cwltool:workflow_job.py:727 [step small_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 4\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 4\n}\nINFO cwltool:workflow_job.py:75 [step small_values_4] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 5\n}\nINFO cwltool:workflow_job.py:572 [step small_values_4] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step big_values_4\nDEBUG cwltool:workflow_job.py:727 [step big_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 4\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_4] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_4] inputs was {\n "i1": 4\n}\nINFO cwltool:workflow_job.py:744 [step big_values_4] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_4] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_4] outputs {\n "obig": null,\n "osmall": 5\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_5] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_5] inputs {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step small_values_5\nDEBUG cwltool:workflow_job.py:727 [step small_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_5] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_5] inputs was {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:744 [step small_values_5] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_5] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step big_values_5\nDEBUG cwltool:workflow_job.py:727 [step big_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 5\n}\nINFO cwltool:workflow_job.py:75 [step big_values_5] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 8\n}\nINFO cwltool:workflow_job.py:572 [step big_values_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_5] outputs {\n "obig": 8,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 8\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_6] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_6] inputs {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step small_values_6\nDEBUG cwltool:workflow_job.py:727 [step small_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_6] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_6] inputs was {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:744 [step small_values_6] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_6] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step big_values_6\nDEBUG cwltool:workflow_job.py:727 [step big_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 8\n}\nINFO cwltool:workflow_job.py:75 [step big_values_6] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 11\n}\nINFO cwltool:workflow_job.py:572 [step big_values_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_6] outputs {\n "obig": 11,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 11\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_7] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_7] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_7] inputs {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step small_values_7\nDEBUG cwltool:workflow_job.py:727 [step small_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_7] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_7] inputs was {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:744 [step small_values_7] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_7] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step big_values_7\nDEBUG cwltool:workflow_job.py:727 [step big_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 11\n}\nINFO cwltool:workflow_job.py:75 [step big_values_7] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 14\n}\nINFO cwltool:workflow_job.py:572 [step big_values_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_7] outputs {\n "obig": 14,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 14\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_8] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_8] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_8] inputs {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_8] starting step small_values_8\nDEBUG cwltool:workflow_job.py:727 [step small_values_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_8] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_8] inputs was {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:744 [step small_values_8] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_8] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_8] starting step big_values_8\nDEBUG cwltool:workflow_job.py:727 [step big_values_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_8] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 14\n}\nINFO cwltool:workflow_job.py:75 [step big_values_8] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 17\n}\nINFO cwltool:workflow_job.py:572 [step big_values_8] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_8] outputs {\n "obig": 17,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 17\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_9] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_9] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_9] inputs {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_9] starting step small_values_9\nDEBUG cwltool:workflow_job.py:727 [step small_values_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_9] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_9] inputs was {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:744 [step small_values_9] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_9] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_9] starting step big_values_9\nDEBUG cwltool:workflow_job.py:727 [step big_values_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 17\n}\nINFO cwltool:workflow_job.py:75 [step big_values_9] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 20\n}\nINFO cwltool:workflow_job.py:572 [step big_values_9] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_9] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_9] outputs {\n "obig": 20,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 20\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop] loop condition $(inputs.i1 < 20) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step loop] inputs was {\n "i1": 20\n}\nDEBUG cwltool:workflow_job.py:564 [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": [\n 2,\n 3,\n 4,\n 5,\n null,\n null,\n null,\n null,\n null\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": [\n null,\n null,\n null,\n null,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {\n "o1": [\n 2,\n 3,\n 4,\n 5,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsrpsturk\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp26tpehja\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpg55oc7b_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbhqm8htr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnnke968d\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpujampaqh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3w_tube1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwdhb0cy6\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsom8y9_3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm4vwtqib\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1180563010002516, 'start': 1685951443.332685, 'stop': 1685951444.450714, '$report_type': 'TestReport', 'item_index': 439, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input', 'location': ('tests/test_loop.py', 249, 'test_multi_source_loop_input'), 'keywords': {'test_multi_source_loop_input': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/multi-source-loop.cwl:60:7: object id \'tests/loop/multi-source-loop.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/multi-source-loop.cwl:61:11: Source \'osmall\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\ntests/loop/multi-source-loop.cwl:61:19: Source \'obig\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _13] start\n\x1b[1;30mINFO\x1b[0m [workflow _13] starting step loop\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step small_values\n\x1b[1;30mINFO\x1b[0m [step small_values] start\n\x1b[1;30mINFO\x1b[0m [step small_values] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step big_values\n\x1b[1;30mINFO\x1b[0m [step big_values] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step small_values_2\n\x1b[1;30mINFO\x1b[0m [step small_values_2] start\n\x1b[1;30mINFO\x1b[0m [step small_values_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step big_values_2\n\x1b[1;30mINFO\x1b[0m [step big_values_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step small_values_3\n\x1b[1;30mINFO\x1b[0m [step small_values_3] start\n\x1b[1;30mINFO\x1b[0m [step small_values_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step big_values_3\n\x1b[1;30mINFO\x1b[0m [step big_values_3] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_3] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step small_values_4\n\x1b[1;30mINFO\x1b[0m [step small_values_4] start\n\x1b[1;30mINFO\x1b[0m [step small_values_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step big_values_4\n\x1b[1;30mINFO\x1b[0m [step big_values_4] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_4] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step small_values_5\n\x1b[1;30mINFO\x1b[0m [step small_values_5] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_5] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step big_values_5\n\x1b[1;30mINFO\x1b[0m [step big_values_5] start\n\x1b[1;30mINFO\x1b[0m [step big_values_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step small_values_6\n\x1b[1;30mINFO\x1b[0m [step small_values_6] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_6] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step big_values_6\n\x1b[1;30mINFO\x1b[0m [step big_values_6] start\n\x1b[1;30mINFO\x1b[0m [step big_values_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step small_values_7\n\x1b[1;30mINFO\x1b[0m [step small_values_7] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_7] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step big_values_7\n\x1b[1;30mINFO\x1b[0m [step big_values_7] start\n\x1b[1;30mINFO\x1b[0m [step big_values_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] starting step small_values_8\n\x1b[1;30mINFO\x1b[0m [step small_values_8] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_8] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] starting step big_values_8\n\x1b[1;30mINFO\x1b[0m [step big_values_8] start\n\x1b[1;30mINFO\x1b[0m [step big_values_8] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] starting step small_values_9\n\x1b[1;30mINFO\x1b[0m [step small_values_9] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_9] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] starting step big_values_9\n\x1b[1;30mINFO\x1b[0m [step big_values_9] start\n\x1b[1;30mINFO\x1b[0m [step big_values_9] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _13] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/multi-source-loop.cwl:60:7: object id \'tests/loop/multi-source-loop.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/multi-source-loop.cwl:61:11: Source \'osmall\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\ntests/loop/multi-source-loop.cwl:61:19: Source \'obig\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step loop\nDEBUG cwltool:workflow_job.py:727 [step loop] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step small_values\nDEBUG cwltool:workflow_job.py:727 [step small_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step small_values] start\nDEBUG cwltool:workflow_job.py:564 [step small_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step small_values] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step big_values\nDEBUG cwltool:workflow_job.py:727 [step big_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop] outputs {\n "obig": null,\n "osmall": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_2] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_2] inputs {\n "i1": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step small_values_2\nDEBUG cwltool:workflow_job.py:727 [step small_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 2\n}\nINFO cwltool:workflow_job.py:75 [step small_values_2] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 3\n}\nINFO cwltool:workflow_job.py:572 [step small_values_2] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step big_values_2\nDEBUG cwltool:workflow_job.py:727 [step big_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 2\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_2] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_2] inputs was {\n "i1": 2\n}\nINFO cwltool:workflow_job.py:744 [step big_values_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_2] outputs {\n "obig": null,\n "osmall": 3\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_3] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_3] inputs {\n "i1": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step small_values_3\nDEBUG cwltool:workflow_job.py:727 [step small_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 3\n}\nINFO cwltool:workflow_job.py:75 [step small_values_3] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 4\n}\nINFO cwltool:workflow_job.py:572 [step small_values_3] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step big_values_3\nDEBUG cwltool:workflow_job.py:727 [step big_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 3\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_3] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_3] inputs was {\n "i1": 3\n}\nINFO cwltool:workflow_job.py:744 [step big_values_3] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_3] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_3] outputs {\n "obig": null,\n "osmall": 4\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_4] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_4] inputs {\n "i1": 4\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step small_values_4\nDEBUG cwltool:workflow_job.py:727 [step small_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 4\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 4\n}\nINFO cwltool:workflow_job.py:75 [step small_values_4] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 5\n}\nINFO cwltool:workflow_job.py:572 [step small_values_4] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step big_values_4\nDEBUG cwltool:workflow_job.py:727 [step big_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 4\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_4] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_4] inputs was {\n "i1": 4\n}\nINFO cwltool:workflow_job.py:744 [step big_values_4] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_4] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_4] outputs {\n "obig": null,\n "osmall": 5\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_5] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_5] inputs {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step small_values_5\nDEBUG cwltool:workflow_job.py:727 [step small_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_5] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_5] inputs was {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:744 [step small_values_5] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_5] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step big_values_5\nDEBUG cwltool:workflow_job.py:727 [step big_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 5\n}\nINFO cwltool:workflow_job.py:75 [step big_values_5] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 8\n}\nINFO cwltool:workflow_job.py:572 [step big_values_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_5] outputs {\n "obig": 8,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 8\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_6] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_6] inputs {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step small_values_6\nDEBUG cwltool:workflow_job.py:727 [step small_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_6] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_6] inputs was {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:744 [step small_values_6] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_6] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step big_values_6\nDEBUG cwltool:workflow_job.py:727 [step big_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 8\n}\nINFO cwltool:workflow_job.py:75 [step big_values_6] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 11\n}\nINFO cwltool:workflow_job.py:572 [step big_values_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_6] outputs {\n "obig": 11,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 11\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_7] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_7] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_7] inputs {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step small_values_7\nDEBUG cwltool:workflow_job.py:727 [step small_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_7] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_7] inputs was {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:744 [step small_values_7] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_7] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step big_values_7\nDEBUG cwltool:workflow_job.py:727 [step big_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 11\n}\nINFO cwltool:workflow_job.py:75 [step big_values_7] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 14\n}\nINFO cwltool:workflow_job.py:572 [step big_values_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_7] outputs {\n "obig": 14,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 14\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_8] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_8] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_8] inputs {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_8] starting step small_values_8\nDEBUG cwltool:workflow_job.py:727 [step small_values_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_8] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_8] inputs was {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:744 [step small_values_8] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_8] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_8] starting step big_values_8\nDEBUG cwltool:workflow_job.py:727 [step big_values_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_8] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 14\n}\nINFO cwltool:workflow_job.py:75 [step big_values_8] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 17\n}\nINFO cwltool:workflow_job.py:572 [step big_values_8] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_8] outputs {\n "obig": 17,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 17\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_9] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_9] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_9] inputs {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_9] starting step small_values_9\nDEBUG cwltool:workflow_job.py:727 [step small_values_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_9] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_9] inputs was {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:744 [step small_values_9] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_9] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_9] starting step big_values_9\nDEBUG cwltool:workflow_job.py:727 [step big_values_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 17\n}\nINFO cwltool:workflow_job.py:75 [step big_values_9] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 20\n}\nINFO cwltool:workflow_job.py:572 [step big_values_9] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_9] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_9] outputs {\n "obig": 20,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 20\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop] loop condition $(inputs.i1 < 20) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step loop] inputs was {\n "i1": 20\n}\nDEBUG cwltool:workflow_job.py:564 [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": [\n 2,\n 3,\n 4,\n 5,\n null,\n null,\n null,\n null,\n null\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": [\n null,\n null,\n null,\n null,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {\n "o1": [\n 2,\n 3,\n 4,\n 5,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsrpsturk\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp26tpehja\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpg55oc7b_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbhqm8htr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnnke968d\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpujampaqh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3w_tube1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwdhb0cy6\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsom8y9_3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm4vwtqib\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000421602999267634, 'start': 1685951444.452204, 'stop': 1685951444.452627, '$report_type': 'TestReport', 'item_index': 439, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_multi_source_loop_input + location: ('tests/test_loop.py', 249, 'test_multi_source_loop_input') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters1-result1]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters1-result1]'), 'keywords': {'test_overrides[parameters1-result1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters1-result1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006827130000601755, 'start': 1685951444.4550772, 'stop': 1685951444.455761, '$report_type': 'TestReport', 'item_index': 468, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides[parameters1-result1] + location: ('tests/test_override.py', 76, 'test_overrides[parameters1-result1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_nproc_expr', 'location': ('tests/test_mpi.py', 154, 'TestMpiRun.test_simple_mpi_nproc_expr'), 'keywords': {'test_simple_mpi_nproc_expr': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job mpi_expr.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_expr.cwl] {\n "processes": 4\n}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_expr.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_expr.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_expr.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_expr.cwl] /private/tmp/docker_tmpaigw30gn$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 4 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_expr.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_expr.cwl] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$05b0c06f1a5d09cb506e00062429a2281b169cb6",\n "size": 24,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_expr.cwl] Removing input staging directory /private/tmp/docker_tmpuhnsmj7a\nDEBUG cwltool:job.py:454 [job mpi_expr.cwl] Removing temporary directory /private/tmp/docker_tmpubimcz5_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_simple_mpi_nproc_expr0/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaigw30gn\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1397649960008494, 'start': 1685951443.578856, 'stop': 1685951444.718595, '$report_type': 'TestReport', 'item_index': 457, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_nproc_expr', 'location': ('tests/test_mpi.py', 154, 'TestMpiRun.test_simple_mpi_nproc_expr'), 'keywords': {'test_simple_mpi_nproc_expr': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job mpi_expr.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_expr.cwl] {\n "processes": 4\n}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_expr.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_expr.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_expr.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_expr.cwl] /private/tmp/docker_tmpaigw30gn$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 4 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_expr.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_expr.cwl] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$05b0c06f1a5d09cb506e00062429a2281b169cb6",\n "size": 24,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_expr.cwl] Removing input staging directory /private/tmp/docker_tmpuhnsmj7a\nDEBUG cwltool:job.py:454 [job mpi_expr.cwl] Removing temporary directory /private/tmp/docker_tmpubimcz5_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_simple_mpi_nproc_expr0/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaigw30gn\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005845309997312143, 'start': 1685951444.719844, 'stop': 1685951444.7204301, '$report_type': 'TestReport', 'item_index': 457, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::TestMpiRun::test_simple_mpi_nproc_expr + location: ('tests/test_mpi.py', 154, 'TestMpiRun.test_simple_mpi_nproc_expr') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::TestMpiRun::test_mpi_workflow + location: ('tests/test_mpi.py', 174, 'TestMpiRun.test_mpi_workflow') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_mpi_workflow', 'location': ('tests/test_mpi.py', 174, 'TestMpiRun.test_mpi_workflow'), 'keywords': {'test_mpi_workflow': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0020967160007785424, 'start': 1685951444.7220821, 'stop': 1685951444.7241821, '$report_type': 'TestReport', 'item_index': 458, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_skip_schemas_external_step', 'location': ('tests/test_misc_cli.py', 67, 'test_skip_schemas_external_step'), 'keywords': {'test_skip_schemas_external_step': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "Warning: Field '$schemas' contains undefined reference to 'https://bad.example.com/missing.ttl'\nWarning: Field '$schemas' contains undefined reference to 'https://schema.org/docs/'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_step_bad_schema.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_step_bad_schema.cwl'\nWARNING salad:ref_resolver.py:1114 Warning: Field '$schemas' contains undefined reference to 'https://bad.example.com/missing.ttl'\nWarning: Field '$schemas' contains undefined reference to 'https://schema.org/docs/'")], 'duration': 0.9561014020000584, 'start': 1685951443.8023129, 'stop': 1685951444.758394, '$report_type': 'TestReport', 'item_index': 452, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_misc_cli.py::test_skip_schemas_external_step', 'location': ('tests/test_misc_cli.py', 67, 'test_skip_schemas_external_step'), 'keywords': {'test_skip_schemas_external_step': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "Warning: Field '$schemas' contains undefined reference to 'https://bad.example.com/missing.ttl'\nWarning: Field '$schemas' contains undefined reference to 'https://schema.org/docs/'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_step_bad_schema.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_step_bad_schema.cwl'\nWARNING salad:ref_resolver.py:1114 Warning: Field '$schemas' contains undefined reference to 'https://bad.example.com/missing.ttl'\nWarning: Field '$schemas' contains undefined reference to 'https://schema.org/docs/'")], 'duration': 0.0003151399996568216, 'start': 1685951444.758986, 'stop': 1685951444.7593029, '$report_type': 'TestReport', 'item_index': 452, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_misc_cli.py::test_skip_schemas_external_step + location: ('tests/test_misc_cli.py', 67, 'test_skip_schemas_external_step') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::test_mpi_conf_defaults + location: ('tests/test_mpi.py', 25, 'test_mpi_conf_defaults') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_defaults', 'location': ('tests/test_mpi.py', 25, 'test_mpi_conf_defaults'), 'keywords': {'test_mpi_conf_defaults': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00028388800001266645, 'start': 1685951444.7607198, 'stop': 1685951444.7610052, '$report_type': 'TestReport', 'item_index': 453, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_defaults', 'location': ('tests/test_mpi.py', 25, 'test_mpi_conf_defaults'), 'keywords': {'test_mpi_conf_defaults': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00022293799975159345, 'start': 1685951444.7613308, 'stop': 1685951444.761555, '$report_type': 'TestReport', 'item_index': 453, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_defaults', 'location': ('tests/test_mpi.py', 25, 'test_mpi_conf_defaults'), 'keywords': {'test_mpi_conf_defaults': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0001631519999136799, 'start': 1685951444.761871, 'stop': 1685951444.762035, '$report_type': 'TestReport', 'item_index': 453, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::test_mpi_conf_defaults + location: ('tests/test_mpi.py', 25, 'test_mpi_conf_defaults') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::test_mpi_conf_unknownkeys + location: ('tests/test_mpi.py', 36, 'test_mpi_conf_unknownkeys') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_unknownkeys', 'location': ('tests/test_mpi.py', 36, 'test_mpi_conf_unknownkeys'), 'keywords': {'test_mpi_conf_unknownkeys': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00022150800032250118, 'start': 1685951444.762811, 'stop': 1685951444.763034, '$report_type': 'TestReport', 'item_index': 454, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_unknownkeys', 'location': ('tests/test_mpi.py', 36, 'test_mpi_conf_unknownkeys'), 'keywords': {'test_mpi_conf_unknownkeys': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006723149999743327, 'start': 1685951444.763655, 'stop': 1685951444.764328, '$report_type': 'TestReport', 'item_index': 454, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_unknownkeys', 'location': ('tests/test_mpi.py', 36, 'test_mpi_conf_unknownkeys'), 'keywords': {'test_mpi_conf_unknownkeys': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00024022699926717905, 'start': 1685951444.7648141, 'stop': 1685951444.765056, '$report_type': 'TestReport', 'item_index': 454, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::test_mpi_conf_unknownkeys + location: ('tests/test_mpi.py', 36, 'test_mpi_conf_unknownkeys') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::TestMpiRun::test_fake_mpi_config + location: ('tests/test_mpi.py', 128, 'TestMpiRun.test_fake_mpi_config') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_fake_mpi_config', 'location': ('tests/test_mpi.py', 128, 'TestMpiRun.test_fake_mpi_config'), 'keywords': {'test_fake_mpi_config': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0038759959998060367, 'start': 1685951444.766158, 'stop': 1685951444.770035, '$report_type': 'TestReport', 'item_index': 455, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_fake_mpi_config', 'location': ('tests/test_mpi.py', 128, 'TestMpiRun.test_fake_mpi_config'), 'keywords': {'test_fake_mpi_config': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.003570607000256132, 'start': 1685951444.770457, 'stop': 1685951444.774029, '$report_type': 'TestReport', 'item_index': 455, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_fake_mpi_config', 'location': ('tests/test_mpi.py', 128, 'TestMpiRun.test_fake_mpi_config'), 'keywords': {'test_fake_mpi_config': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007795419996909914, 'start': 1685951444.774543, 'stop': 1685951444.7753248, '$report_type': 'TestReport', 'item_index': 455, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::TestMpiRun::test_fake_mpi_config + location: ('tests/test_mpi.py', 128, 'TestMpiRun.test_fake_mpi_config') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl] + location: ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]', 'location': ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]'), 'keywords': {'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/hello-workflow.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003464189994701883, 'start': 1685951444.776302, 'stop': 1685951444.77665, '$report_type': 'TestReport', 'item_index': 489, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_hint', 'location': ('tests/test_loop.py', 89, 'test_validate_loop_fail_on_hint'), 'keywords': {'test_validate_loop_fail_on_hint': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-hint.cwl:26:7: object id \'tests/loop/invalid-loop-hint.cwl#subworkflow/i1\' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mValidation failed at\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1048, in validate_hints\n raise ValidationException(\nschema_salad.exceptions.ValidationException: http://commonwl.org/cwltool#Loop is valid only under requirements.\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 107, in __init__\n self.make_workflow_step(step, index, loadingContext, loadingContext.prov_obj)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 152, in make_workflow_step\n return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 347, in __init__\n super().__init__(toolpath_object, loadingContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 603, in __init__\n self.validate_hints(\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1045, in validate_hints\n with sl:\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/sourceline.py", line 250, in __exit__\n raise self.makeError(str(exc_value)) from exc_value\nschema_salad.exceptions.ValidationException: tests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-hint.cwl:26:7: object id \'tests/loop/invalid-loop-hint.cwl#subworkflow/i1\' previously defined\nERROR cwltool:workflow.py:111 Validation failed at\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1048, in validate_hints\n raise ValidationException(\nschema_salad.exceptions.ValidationException: http://commonwl.org/cwltool#Loop is valid only under requirements.\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 107, in __init__\n self.make_workflow_step(step, index, loadingContext, loadingContext.prov_obj)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 152, in make_workflow_step\n return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 347, in __init__\n super().__init__(toolpath_object, loadingContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 603, in __init__\n self.validate_hints(\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1045, in validate_hints\n with sl:\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/sourceline.py", line 250, in __exit__\n raise self.makeError(str(exc_value)) from exc_value\nschema_salad.exceptions.ValidationException: tests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.')], 'duration': 0.8786398969996299, 'start': 1685951443.930252, 'stop': 1685951444.808871, '$report_type': 'TestReport', 'item_index': 426, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_hint', 'location': ('tests/test_loop.py', 89, 'test_validate_loop_fail_on_hint'), 'keywords': {'test_validate_loop_fail_on_hint': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-hint.cwl:26:7: object id \'tests/loop/invalid-loop-hint.cwl#subworkflow/i1\' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mValidation failed at\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1048, in validate_hints\n raise ValidationException(\nschema_salad.exceptions.ValidationException: http://commonwl.org/cwltool#Loop is valid only under requirements.\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 107, in __init__\n self.make_workflow_step(step, index, loadingContext, loadingContext.prov_obj)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 152, in make_workflow_step\n return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 347, in __init__\n super().__init__(toolpath_object, loadingContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 603, in __init__\n self.validate_hints(\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1045, in validate_hints\n with sl:\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/sourceline.py", line 250, in __exit__\n raise self.makeError(str(exc_value)) from exc_value\nschema_salad.exceptions.ValidationException: tests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-hint.cwl:26:7: object id \'tests/loop/invalid-loop-hint.cwl#subworkflow/i1\' previously defined\nERROR cwltool:workflow.py:111 Validation failed at\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1048, in validate_hints\n raise ValidationException(\nschema_salad.exceptions.ValidationException: http://commonwl.org/cwltool#Loop is valid only under requirements.\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 107, in __init__\n self.make_workflow_step(step, index, loadingContext, loadingContext.prov_obj)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 152, in make_workflow_step\n return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 347, in __init__\n super().__init__(toolpath_object, loadingContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 603, in __init__\n self.validate_hints(\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1045, in validate_hints\n with sl:\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/sourceline.py", line 250, in __exit__\n raise self.makeError(str(exc_value)) from exc_value\nschema_salad.exceptions.ValidationException: tests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.')], 'duration': 0.0003478279995761113, 'start': 1685951444.8094342, 'stop': 1685951444.809783, '$report_type': 'TestReport', 'item_index': 426, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_validate_loop_fail_on_hint + location: ('tests/test_loop.py', 89, 'test_validate_loop_fail_on_hint') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_fail_non_boolean_loop_when', 'location': ('tests/test_loop.py', 99, 'test_loop_fail_non_boolean_loop_when'), 'keywords': {'test_loop_fail_non_boolean_loop_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00019406599949434167, 'start': 1685951444.8108952, 'stop': 1685951444.8110888, '$report_type': 'TestReport', 'item_index': 427, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_loop_fail_non_boolean_loop_when + location: ('tests/test_loop.py', 99, 'test_loop_fail_non_boolean_loop_when') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]', 'location': ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]'), 'keywords': {'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/hello-workflow.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'")], 'duration': 0.046458136000183003, 'start': 1685951444.777009, 'stop': 1685951444.823467, '$report_type': 'TestReport', 'item_index': 489, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]', 'location': ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]'), 'keywords': {'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/hello-workflow.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'")], 'duration': 0.00031945299997460097, 'start': 1685951444.8240378, 'stop': 1685951444.824359, '$report_type': 'TestReport', 'item_index': 489, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl] + location: ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_pack_idempotence_tool + location: ('tests/test_pack.py', 138, 'test_pack_idempotence_tool') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_idempotence_tool', 'location': ('tests/test_pack.py', 138, 'test_pack_idempotence_tool'), 'keywords': {'test_pack_idempotence_tool': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011834360002467292, 'start': 1685951444.825451, 'stop': 1685951444.826636, '$report_type': 'TestReport', 'item_index': 490, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_idempotence_tool', 'location': ('tests/test_pack.py', 138, 'test_pack_idempotence_tool'), 'keywords': {'test_pack_idempotence_tool': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_tool0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_tool0/packed.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_tool0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_tool0/packed.cwl'")], 'duration': 0.04199383000013768, 'start': 1685951444.827132, 'stop': 1685951444.8691258, '$report_type': 'TestReport', 'item_index': 490, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_pack_idempotence_tool + location: ('tests/test_pack.py', 138, 'test_pack_idempotence_tool') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_pack_idempotence_workflow + location: ('tests/test_pack.py', 143, 'test_pack_idempotence_workflow') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_idempotence_workflow', 'location': ('tests/test_pack.py', 143, 'test_pack_idempotence_workflow'), 'keywords': {'test_pack_idempotence_workflow': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0010339679993194295, 'start': 1685951444.870764, 'stop': 1685951444.871799, '$report_type': 'TestReport', 'item_index': 491, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] +",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$05b0c06f1a5d09cb506e00062429a2281b169cb6",\n "size": 24,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_expr.cwl] Removing input staging directory /private/tmp/docker_tmpuhnsmj7a\nDEBUG cwltool:job.py:454 [job mpi_expr.cwl] Removing temporary directory /private/tmp/docker_tmpubimcz5_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_simple_mpi_nproc_expr0/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaigw30gn\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1397649960008494, 'start': 1685951443.578856, 'stop': 1685951444.718595, '$report_type': 'TestReport', 'item_index': 457, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} +pŒmðŸX0±\0?SðŸX0?S0=Sð]]Ú§Xر3=S0¹Q°½Xð]]ðŸX°JT0^]0?S0§X°½XðwTð¦X0±\0^]ð]]0§X0§X0FTðªQð¦Xð#\ð]]°>S°Óm°ÄZ°>S°ÄZ°ÄZ°>S°dp^]0§X°½XðwTð¦X0±\°d0Œm0§X0?S0¹QðI^ð]]ð]]0Œm°d0§X°œQ°dðŸXðÙm0FT0±\°dp+_ptðŸXðÙm0FT0±\ptÚdšƒØ±±I^ðwTðwTðI^ðÙm809891'} +er.io/everpeace/curl-jq\']\nUsing default tag: latest\nlatest: Pulling from everpeace/curl-jq\nDigest: sha256:913ca8896b01799201a1eeb9ddf9 pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_passthrough_successive', 'location': ('tests/test_iwdr.py', 29, 'test_passthrough_successive'), 'keywords': {'test_passthrough_successive': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _2] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1 not ready\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step mkdirs\nDEBUG cwltool:workflow_job.py:727 [step mkdirs] job input {}\nDEBUG cwltool:workflow_job.py:732 [step mkdirs] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step mkdirs] start\nDEBUG cwltool:command_line_tool.py:982 [job mkdirs] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#mkdirs/2b25f995-b05d-4dcf-a9bc-f2418a66296d as part of step mkdirs\nDEBUG cwltool:command_line_tool.py:988 [job mkdirs] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mkdirs] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mkdirs] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "mkdir dir dir/subdir && touch dir/subdir/file"\n },\n {\n "position": [\n -1000000,\n 3\n ],\n "datum": "-"\n }\n]\nDEBUG cwltool:job.py:215 [job mkdirs] initial work dir {}\nINFO cwltool:job.py:266 [job mkdirs] /private/tmp/docker_tmpijyeq8bv$ bash \\\n -c \\\n \'mkdir dir dir/subdir && touch dir/subdir/file\' \\\n -\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mkdirs] completed success\nDEBUG cwltool:job.py:422 [job mkdirs] outputs {\n "mkdirs_out": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step mkdirs] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#mkdirs/mkdirs_out": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step mkdirs] completed success\nDEBUG cwltool:job.py:446 [job mkdirs] Removing input staging directory /private/tmp/docker_tmphrcu_ih1\nDEBUG cwltool:job.py:454 [job mkdirs] Removing temporary directory /private/tmp/docker_tmp_h9cg8p2\nDEBUG cwltool:workflow_job.py:610 [workflow _2] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2 not ready\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step passthrough1\nDEBUG cwltool:workflow_job.py:727 [step passthrough1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step passthrough1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:75 [step passthrough1] start\nDEBUG cwltool:command_line_tool.py:982 [job passthrough1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/7a196622-4d49-479f-a3b1-df60a7883de2 as part of step passthrough1\nDEBUG cwltool:command_line_tool.py:988 [job passthrough1] {\n "passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "basename": "file",\n "size": 0\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job passthrough1] path mappings is {\n "file:///private/tmp/docker_tmpijyeq8bv/dir": [\n "/private/tmp/docker_tmpijyeq8bv/dir",\n "/private/tmp/docker_tmpso0k9rfa/dir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir/file",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job passthrough1] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job passthrough1] initial work dir {\n "file:///private/tmp/docker_tmpijyeq8bv/dir": [\n "/private/tmp/docker_tmpijyeq8bv/dir",\n "/private/tmp/docker_tmpso0k9rfa/dir",\n "Directory",\n true\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir/file",\n "File",\n false\n ]\n}\nINFO cwltool:job.py:266 [job passthrough1] /private/tmp/docker_tmpso0k9rfa$ true\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job passthrough1] completed success\nDEBUG cwltool:job.py:422 [job passthrough1] outputs {\n "passthrough1_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step passthrough1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step passthrough1] completed success\nDEBUG cwltool:job.py:446 [job passthrough1] Removing input staging directory /private/tmp/docker_tmpg2ol4k_l\nDEBUG cwltool:job.py:454 [job passthrough1] Removing temporary directory /private/tmp/docker_tmpm9x2m7gy\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step passthrough2\nDEBUG cwltool:workflow_job.py:727 [step passthrough2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step passthrough2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:75 [step passthrough2] start\nDEBUG cwltool:command_line_tool.py:982 [job passthrough2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/fab92b9c-ed66-45ae-ae7f-411f0edd6009 as part of step passthrough2\nDEBUG cwltool:command_line_tool.py:988 [job passthrough2] {\n "passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "basename": "file",\n "size": 0\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job passthrough2] path mappings is {\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmp1p6du01p/subdir",\n "Directory",\n false\n ],\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmp1p6du01p/subdir/file",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job passthrough2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job passthrough2] initial work dir {\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmp1p6du01p/subdir",\n "Directory",\n true\n ],\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmp1p6du01p/subdir/file",\n "File",\n true\n ]\n}\nINFO cwltool:job.py:266 [job passthrough2] /private/tmp/docker_tmp1p6du01p$ true\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job passthrough2] completed success\nDEBUG cwltool:job.py:422 [job passthrough2] outputs {\n "passthrough2_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step passthrough2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step passthrough2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {\n "out": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job passthrough2] Removing input staging directory /private/tmp/docker_tmpjmoq_pe2\nDEBUG cwltool:job.py:454 [job passthrough2] Removing temporary directory /private/tmp/docker_tmp1dce8v2z\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpijyeq8bv/dir/subdir to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw0/test_passthrough_successive0/subdir\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1p6du01p\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa3js7lcr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpso0k9rfa\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpijyeq8bv\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.778309483999692, 'start': 1685951444.1388621, 'stop': 1685951444.917154, '$report_type': 'TestReport', 'item_index': 393, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_iwdr.py::test_passthrough_successive', 'location': ('tests/test_iwdr.py', 29, 'test_passthrough_successive'), 'keywords': {'test_passthrough_successive': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _2] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1 not ready\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step mkdirs\nDEBUG cwltool:workflow_job.py:727 [step mkdirs] job input {}\nDEBUG cwltool:workflow_job.py:732 [step mkdirs] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step mkdirs] start\nDEBUG cwltool:command_line_tool.py:982 [job mkdirs] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#mkdirs/2b25f995-b05d-4dcf-a9bc-f2418a66296d as part of step mkdirs\nDEBUG cwltool:command_line_tool.py:988 [job mkdirs] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mkdirs] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mkdirs] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "mkdir dir dir/subdir && touch dir/subdir/file"\n },\n {\n "position": [\n -1000000,\n 3\n ],\n "datum": "-"\n }\n]\nDEBUG cwltool:job.py:215 [job mkdirs] initial work dir {}\nINFO cwltool:job.py:266 [job mkdirs] /private/tmp/docker_tmpijyeq8bv$ bash \\\n -c \\\n \'mkdir dir dir/subdir && touch dir/subdir/file\' \\\n -\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mkdirs] completed success\nDEBUG cwltool:job.py:422 [job mkdirs] outputs {\n "mkdirs_out": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step mkdirs] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#mkdirs/mkdirs_out": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step mkdirs] completed success\nDEBUG cwltool:job.py:446 [job mkdirs] Removing input staging directory /private/tmp/docker_tmphrcu_ih1\nDEBUG cwltool:job.py:454 [job mkdirs] Removing temporary directory /private/tmp/docker_tmp_h9cg8p2\nDEBUG cwltool:workflow_job.py:610 [workflow _2] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2 not ready\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step passthrough1\nDEBUG cwltool:workflow_job.py:727 [step passthrough1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step passthrough1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:75 [step passthrough1] start\nDEBUG cwltool:command_line_tool.py:982 [job passthrough1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/7a196622-4d49-479f-a3b1-df60a7883de2 as part of step passthrough1\nDEBUG cwltool:command_line_tool.py:988 [job passthrough1] {\n "passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "basename": "file",\n "size": 0\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job passthrough1] path mappings is {\n "file:///private/tmp/docker_tmpijyeq8bv/dir": [\n "/private/tmp/docker_tmpijyeq8bv/dir",\n "/private/tmp/docker_tmpso0k9rfa/dir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir/file",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job passthrough1] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job passthrough1] initial work dir {\n "file:///private/tmp/docker_tmpijyeq8bv/dir": [\n "/private/tmp/docker_tmpijyeq8bv/dir",\n "/private/tmp/docker_tmpso0k9rfa/dir",\n "Directory",\n true\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir/file",\n "File",\n false\n ]\n}\nINFO cwltool:job.py:266 [job passthrough1] /private/tmp/docker_tmpso0k9rfa$ true\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job passthrough1] completed success\nDEBUG cwltool:job.py:422 [job passthrough1] outputs {\n "passthrough1_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step passthrough1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step passthrough1] completed success\nDEBUG cwltool:job.py:446 [job passthrough1] Removing input staging directory /private/tmp/docker_tmpg2ol4k_l\nDEBUG cwltool:job.py:454 [job passthrough1] Removing temporary directory /private/tmp/docker_tmpm9x2m7gy\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step passthrough2\nDEBUG cwltool:workflow_job.py:727 [step passthrough2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step passthrough2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:75 [step passthrough2] start\nDEBUG cwltool:command_line_tool.py:982 [job passthrough2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/fab92b9c-ed66-45ae-ae7f-411f0edd6009 as part of step passthrough2\nDEBUG cwltool:command_line_tool.py:988 [job passthrough2] {\n "passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "basename": "file",\n "size": 0\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job passthrough2] path mappings is {\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmp1p6du01p/subdir",\n "Directory",\n false\n ],\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmp1p6du01p/subdir/file",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job passthrough2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job passthrough2] initial work dir {\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmp1p6du01p/subdir",\n "Directory",\n true\n ],\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmp1p6du01p/subdir/file",\n "File",\n true\n ]\n}\nINFO cwltool:job.py:266 [job passthrough2] /private/tmp/docker_tmp1p6du01p$ true\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job passthrough2] completed success\nDEBUG cwltool:job.py:422 [job passthrough2] outputs {\n "passthrough2_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step passthrough2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step passthrough2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {\n "out": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job passthrough2] Removing input staging directory /private/tmp/docker_tmpjmoq_pe2\nDEBUG cwltool:job.py:454 [job passthrough2] Removing temporary directory /private/tmp/docker_tmp1dce8v2z\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpijyeq8bv/dir/subdir to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw0/test_passthrough_successive0/subdir\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1p6du01p\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa3js7lcr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpso0k9rfa\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpijyeq8bv\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005935129993304145, 'start': 1685951444.918226, 'stop': 1685951444.918821, '$report_type': 'TestReport', 'item_index': 393, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_iwdr.py::test_passthrough_successive + location: ('tests/test_iwdr.py', 29, 'test_passthrough_successive') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.] + location: ('tests/test_override.py', 119, "test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]") + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007491690003007534, 'start': 1685951444.920224, 'stop': 1685951444.920974, '$report_type': 'TestReport', 'item_index': 479, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_idempotence_workflow', 'location': ('tests/test_pack.py', 143, 'test_pack_idempotence_workflow'), 'keywords': {'test_pack_idempotence_workflow': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl'")], 'duration': 0.16907998900023813, 'start': 1685951444.8721511, 'stop': 1685951445.041229, '$report_type': 'TestReport', 'item_index': 491, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_idempotence_workflow', 'location': ('tests/test_pack.py', 143, 'test_pack_idempotence_workflow'), 'keywords': {'test_pack_idempotence_workflow': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl'")], 'duration': 0.0005268760005492368, 'start': 1685951445.041944, 'stop': 1685951445.042474, '$report_type': 'TestReport', 'item_index': 491, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_pack_idempotence_workflow + location: ('tests/test_pack.py', 143, 'test_pack_idempotence_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False] + location: ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]'), 'keywords': {'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015690330001234543, 'start': 1685951445.043638, 'stop': 1685951445.045208, '$report_type': 'TestReport', 'item_index': 492, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters1-result1]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters1-result1]'), 'keywords': {'test_overrides[parameters1-result1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters1-result1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_3] /private/tmp/docker_tmpzeavrjm9$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpzeavrjm9/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_3] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_3] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_3] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_3] /private/tmp/docker_tmpzeavrjm9$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpzeavrjm9/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_3] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_3] Removing input staging directory /private/tmp/docker_tmpu4_tqu0y\nDEBUG cwltool:job.py:454 [job echo.cwl_3] Removing temporary directory /private/tmp/docker_tmpij4rzbsm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzeavrjm9\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7023725059998469, 'start': 1685951444.456256, 'stop': 1685951445.158613, '$report_type': 'TestReport', 'item_index': 468, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters1-result1]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters1-result1]'), 'keywords': {'test_overrides[parameters1-result1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters1-result1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_3] /private/tmp/docker_tmpzeavrjm9$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpzeavrjm9/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_3] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_3] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_3] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_3] /private/tmp/docker_tmpzeavrjm9$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpzeavrjm9/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_3] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_3] Removing input staging directory /private/tmp/docker_tmpu4_tqu0y\nDEBUG cwltool:job.py:454 [job echo.cwl_3] Removing temporary directory /private/tmp/docker_tmpij4rzbsm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzeavrjm9\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0012532579994513071, 'start': 1685951445.160028, 'stop': 1685951445.1612842, '$report_type': 'TestReport', 'item_index': 468, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides[parameters1-result1] + location: ('tests/test_override.py', 76, 'test_overrides[parameters1-result1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides[parameters2-result2] + location: ('tests/test_override.py', 76, 'test_overrides[parameters2-result2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters2-result2]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters2-result2]'), 'keywords': {'test_overrides[parameters2-result2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-result2': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001179238999611698, 'start': 1685951445.1633039, 'stop': 1685951445.1644852, '$report_type': 'TestReport', 'item_index': 469, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nVersion 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.")], 'duration': 0.7835435590004636, 'start': 1685951444.921406, 'stop': 1685951445.7049322, '$report_type': 'TestReport', 'item_index': 479, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nVersion 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.")], 'duration': 0.0006185950005601626, 'start': 1685951445.7059588, 'stop': 1685951445.70658, '$report_type': 'TestReport', 'item_index': 479, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.] + location: ('tests/test_override.py', 119, "test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl] + location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort.cwl-tests/wf/expect_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005526220002138871, 'start': 1685951445.708649, 'stop': 1685951445.709203, '$report_type': 'TestReport', 'item_index': 480, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_fail_non_boolean_loop_when', 'location': ('tests/test_loop.py', 99, 'test_loop_fail_non_boolean_loop_when'), 'keywords': {'test_loop_fail_non_boolean_loop_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "o1": null\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-non-boolean-loopWhen.cwl:32:11: object id 'tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _12] start\n\x1b[1;30mINFO\x1b[0m [workflow _12] starting step subworkflow\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step subworkflow] Cannot make job: Loop condition 'loopWhen' must evaluate to 'true' or 'false'\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _12] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-non-boolean-loopWhen.cwl:32:11: object id \'tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step subworkflow\nDEBUG cwltool:workflow_job.py:727 [step subworkflow] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i2": 1\n}\nERROR cwltool:workflow_job.py:833 [step subworkflow] Cannot make job: Loop condition \'loopWhen\' must evaluate to \'true\' or \'false\'\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 751, in try_make_job\n yield from jobs\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 936, in job\n raise WorkflowException(\ncwltool.errors.WorkflowException: Loop condition \'loopWhen\' must evaluate to \'true\' or \'false\'\nINFO cwltool:workflow_job.py:539 [workflow _12] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {\n "o1": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbnn_geot\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.9484818880000603, 'start': 1685951444.811543, 'stop': 1685951445.7600021, '$report_type': 'TestReport', 'item_index': 427, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_fail_non_boolean_loop_when', 'location': ('tests/test_loop.py', 99, 'test_loop_fail_non_boolean_loop_when'), 'keywords': {'test_loop_fail_non_boolean_loop_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "o1": null\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-non-boolean-loopWhen.cwl:32:11: object id 'tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _12] start\n\x1b[1;30mINFO\x1b[0m [workflow _12] starting step subworkflow\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step subworkflow] Cannot make job: Loop condition 'loopWhen' must evaluate to 'true' or 'false'\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _12] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-non-boolean-loopWhen.cwl:32:11: object id \'tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step subworkflow\nDEBUG cwltool:workflow_job.py:727 [step subworkflow] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i2": 1\n}\nERROR cwltool:workflow_job.py:833 [step subworkflow] Cannot make job: Loop condition \'loopWhen\' must evaluate to \'true\' or \'false\'\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 751, in try_make_job\n yield from jobs\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 936, in job\n raise WorkflowException(\ncwltool.errors.WorkflowException: Loop condition \'loopWhen\' must evaluate to \'true\' or \'false\'\nINFO cwltool:workflow_job.py:539 [workflow _12] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {\n "o1": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbnn_geot\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.000542493000466493, 'start': 1685951445.7606468, 'stop': 1685951445.761191, '$report_type': 'TestReport', 'item_index': 427, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_loop_fail_non_boolean_loop_when + location: ('tests/test_loop.py', 99, 'test_loop_fail_non_boolean_loop_when') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_loop_single_variable + location: ('tests/test_loop.py', 109, 'test_loop_single_variable') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable', 'location': ('tests/test_loop.py', 109, 'test_loop_single_variable'), 'keywords': {'test_loop_single_variable': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00030629299999418436, 'start': 1685951445.762482, 'stop': 1685951445.76279, '$report_type': 'TestReport', 'item_index': 428, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters2-result2]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters2-result2]'), 'keywords': {'test_overrides[parameters2-result2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-result2': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_4] /private/tmp/docker_tmp8c1vt_no$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp8c1vt_no/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_4] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_4] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_4] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_4] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_4] /private/tmp/docker_tmp8c1vt_no$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp8c1vt_no/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_4] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_4] outputs {\n "out": "zing hello3\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_4] Removing input staging directory /private/tmp/docker_tmp0re0kkyy\nDEBUG cwltool:job.py:454 [job echo.cwl_4] Removing temporary directory /private/tmp/docker_tmptk7mihrz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp8c1vt_no\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.71063700600007, 'start': 1685951445.165343, 'stop': 1685951445.8759658, '$report_type': 'TestReport', 'item_index': 469, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters2-result2]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters2-result2]'), 'keywords': {'test_overrides[parameters2-result2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-result2': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_4] /private/tmp/docker_tmp8c1vt_no$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp8c1vt_no/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_4] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_4] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_4] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_4] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_4] /private/tmp/docker_tmp8c1vt_no$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp8c1vt_no/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_4] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_4] outputs {\n "out": "zing hello3\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_4] Removing input staging directory /private/tmp/docker_tmp0re0kkyy\nDEBUG cwltool:job.py:454 [job echo.cwl_4] Removing temporary directory /private/tmp/docker_tmptk7mihrz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp8c1vt_no\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007379569997283397, 'start': 1685951445.8771148, 'stop': 1685951445.877855, '$report_type': 'TestReport', 'item_index': 469, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides[parameters2-result2] + location: ('tests/test_override.py', 76, 'test_overrides[parameters2-result2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides[parameters3-result3] + location: ('tests/test_override.py', 76, 'test_overrides[parameters3-result3]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters3-result3]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters3-result3]'), 'keywords': {'test_overrides[parameters3-result3]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters3-result3': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008628899995528627, 'start': 1685951445.879502, 'stop': 1685951445.880367, '$report_type': 'TestReport', 'item_index': 470, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_mpi_workflow', 'location': ('tests/test_mpi.py', 174, 'TestMpiRun.test_mpi_workflow'), 'keywords': {'test_mpi_workflow': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "processes": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step par_pids\nDEBUG cwltool:workflow_job.py:727 [step par_pids] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/processes": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step par_pids] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/processes": 3\n}\nINFO cwltool:workflow_job.py:75 [step par_pids] start\nDEBUG cwltool:command_line_tool.py:982 [job par_pids] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl as part of step par_pids\nDEBUG cwltool:command_line_tool.py:988 [job par_pids] {\n "processes": 3\n}\nDEBUG cwltool:command_line_tool.py:1000 [job par_pids] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job par_pids] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job par_pids] initial work dir {}\nINFO cwltool:job.py:266 [job par_pids] /private/tmp/docker_tmp85u5ffmq$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 3 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job par_pids] completed success\nDEBUG cwltool:job.py:422 [job par_pids] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step par_pids] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/pids": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step par_pids] completed success\nDEBUG cwltool:job.py:446 [job par_pids] Removing input staging directory /private/tmp/docker_tmppt3kvz7k\nDEBUG cwltool:job.py:454 [job par_pids] Removing temporary directory /private/tmp/docker_tmpc8nr7b2m\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step count\nDEBUG cwltool:workflow_job.py:727 [step count] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step count] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step count] start\nDEBUG cwltool:command_line_tool.py:982 [job count] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_line_count.cwl as part of step count\nDEBUG cwltool:command_line_tool.py:988 [job count] {\n "pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count] path mappings is {\n "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8": [\n "/private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "/private/tmp/docker_tmp7lqo6r6u/stg2cb31d92-a49d-40a8-b109-fcc66ba5559b/46516be4494917870bf55e45a1047abf0da9e0b8",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count] initial work dir {}\nINFO cwltool:job.py:266 [job count] /private/tmp/docker_tmp6x96v1_p$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 1 \\\n --no-fail \\\n wc \\\n -l < /private/tmp/docker_tmp7lqo6r6u/stg2cb31d92-a49d-40a8-b109-fcc66ba5559b/46516be4494917870bf55e45a1047abf0da9e0b8 > /private/tmp/docker_tmp6x96v1_p/line_count\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job count] completed success\nDEBUG cwltool:job.py:422 [job count] outputs {\n "line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step count] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step count] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count] Removing input staging directory /private/tmp/docker_tmp7lqo6r6u\nDEBUG cwltool:job.py:454 [job count] Removing temporary directory /private/tmp/docker_tmp4b2tpt7w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6x96v1_p/line_count to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_mpi_workflow0/line_count\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp85u5ffmq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpne46mazt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6x96v1_p\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.3001793530002033, 'start': 1685951444.7247481, 'stop': 1685951446.024896, '$report_type': 'TestReport', 'item_index': 458, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_mpi_workflow', 'location': ('tests/test_mpi.py', 174, 'TestMpiRun.test_mpi_workflow'), 'keywords': {'test_mpi_workflow': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "processes": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step par_pids\nDEBUG cwltool:workflow_job.py:727 [step par_pids] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/processes": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step par_pids] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/processes": 3\n}\nINFO cwltool:workflow_job.py:75 [step par_pids] start\nDEBUG cwltool:command_line_tool.py:982 [job par_pids] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl as part of step par_pids\nDEBUG cwltool:command_line_tool.py:988 [job par_pids] {\n "processes": 3\n}\nDEBUG cwltool:command_line_tool.py:1000 [job par_pids] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job par_pids] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job par_pids] initial work dir {}\nINFO cwltool:job.py:266 [job par_pids] /private/tmp/docker_tmp85u5ffmq$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 3 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job par_pids] completed success\nDEBUG cwltool:job.py:422 [job par_pids] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step par_pids] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/pids": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step par_pids] completed success\nDEBUG cwltool:job.py:446 [job par_pids] Removing input staging directory /private/tmp/docker_tmppt3kvz7k\nDEBUG cwltool:job.py:454 [job par_pids] Removing temporary directory /private/tmp/docker_tmpc8nr7b2m\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step count\nDEBUG cwltool:workflow_job.py:727 [step count] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step count] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step count] start\nDEBUG cwltool:command_line_tool.py:982 [job count] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_line_count.cwl as part of step count\nDEBUG cwltool:command_line_tool.py:988 [job count] {\n "pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count] path mappings is {\n "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8": [\n "/private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "/private/tmp/docker_tmp7lqo6r6u/stg2cb31d92-a49d-40a8-b109-fcc66ba5559b/46516be4494917870bf55e45a1047abf0da9e0b8",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count] initial work dir {}\nINFO cwltool:job.py:266 [job count] /private/tmp/docker_tmp6x96v1_p$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 1 \\\n --no-fail \\\n wc \\\n -l < /private/tmp/docker_tmp7lqo6r6u/stg2cb31d92-a49d-40a8-b109-fcc66ba5559b/46516be4494917870bf55e45a1047abf0da9e0b8 > /private/tmp/docker_tmp6x96v1_p/line_count\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job count] completed success\nDEBUG cwltool:job.py:422 [job count] outputs {\n "line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step count] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step count] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count] Removing input staging directory /private/tmp/docker_tmp7lqo6r6u\nDEBUG cwltool:job.py:454 [job count] Removing temporary directory /private/tmp/docker_tmp4b2tpt7w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6x96v1_p/line_count to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_mpi_workflow0/line_count\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp85u5ffmq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpne46mazt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6x96v1_p\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006665989994871779, 'start': 1685951446.0263638, 'stop': 1685951446.0270321, '$report_type': 'TestReport', 'item_index': 458, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::TestMpiRun::test_mpi_workflow + location: ('tests/test_mpi.py', 174, 'TestMpiRun.test_mpi_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::TestMpiRun::test_environment + location: ('tests/test_mpi.py', 194, 'TestMpiRun.test_environment') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_environment', 'location': ('tests/test_mpi.py', 194, 'TestMpiRun.test_environment'), 'keywords': {'test_environment': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001445703000172216, 'start': 1685951446.028768, 'stop': 1685951446.030216, '$report_type': 'TestReport', 'item_index': 459, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort.cwl-tests/wf/expect_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:45]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'")], 'duration': 0.7957583910001631, 'start': 1685951445.709607, 'stop': 1685951446.505347, '$report_type': 'TestReport', 'item_index': 480, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort.cwl-tests/wf/expect_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:45]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'")], 'duration': 0.00042291299996577436, 'start': 1685951446.506038, 'stop': 1685951446.5064619, '$report_type': 'TestReport', 'item_index': 480, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl] + location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl] + location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]'), 'keywords': {'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006471120004789555, 'start': 1685951446.507751, 'stop': 1685951446.508399, '$report_type': 'TestReport', 'item_index': 481, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_write_write_conflict', 'location': ('tests/test_ext.py', 207, 'test_write_write_conflict'), 'keywords': {'test_write_write_conflict': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m [workflow _2] start\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step step2_2\n\x1b[1;30mINFO\x1b[0m [step step2_2] start\n\x1b[1;30mINFO\x1b[0m [job step2_2] /private/tmp/docker_tmpptsgalmt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpptsgalmt,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp4qbnegg7,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmhfpqlte/20230605095045-609224.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step2_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mERROR\x1b[0m \x1b[31mException on step 'step1'\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step step1_2] Cannot make job: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _2] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl",\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value"\n }\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step step2_2\nDEBUG cwltool:workflow_job.py:727 [step step2_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step2/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step2/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step2_2\nDEBUG cwltool:command_line_tool.py:988 [job step2_2] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step2_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step2_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job step2_2] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step2_2] /private/tmp/docker_tmpptsgalmt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpptsgalmt,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp4qbnegg7,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmhfpqlte/20230605095045-609224.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step2_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step2_2] completed success\nDEBUG cwltool:job.py:422 [job step2_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpptsgalmt/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_2] produced output {}\nINFO cwltool:workflow_job.py:572 [step step2_2] completed success\nDEBUG cwltool:job.py:446 [job step2_2] Removing input staging directory /private/tmp/docker_tmpi7dfk_9x\nDEBUG cwltool:job.py:454 [job step2_2] Removing temporary directory /private/tmp/docker_tmp4qbnegg7\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgef2bfe92-5a62-4b36-b8ec-96b99ea4527f/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nERROR cwltool:workflow.py:465 Exception on step \'step1\'\nERROR cwltool:workflow_job.py:833 [step step1_2] Cannot make job: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 751, in try_make_job\n yield from jobs\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 77, in job\n yield from self.step.job(joborder, output_callback, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 459, in job\n yield from self.embedded_tool.job(\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 1090, in job\n adjustFileObjs(li, register_mut)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 273, in adjustFileObjs\n visit_class(rec, ("File",), op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 1080, in register_mut\n mm.register_mutation(j.name, f)\n File "/Users/jasperk/gitlab/cwltool/cwltool/mutation.py", line 69, in register_mutation\n raise WorkflowException(\ncwltool.errors.WorkflowException: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\nINFO cwltool:workflow_job.py:539 [workflow _2] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpptsgalmt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwij4jvx9\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 2.6720536889997675, 'start': 1685951443.967964, 'stop': 1685951446.6399539, '$report_type': 'TestReport', 'item_index': 374, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_write_write_conflict', 'location': ('tests/test_ext.py', 207, 'test_write_write_conflict'), 'keywords': {'test_write_write_conflict': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m [workflow _2] start\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step step2_2\n\x1b[1;30mINFO\x1b[0m [step step2_2] start\n\x1b[1;30mINFO\x1b[0m [job step2_2] /private/tmp/docker_tmpptsgalmt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpptsgalmt,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp4qbnegg7,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmhfpqlte/20230605095045-609224.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step2_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mERROR\x1b[0m \x1b[31mException on step 'step1'\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step step1_2] Cannot make job: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _2] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl",\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value"\n }\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step step2_2\nDEBUG cwltool:workflow_job.py:727 [step step2_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step2/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step2/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step2_2\nDEBUG cwltool:command_line_tool.py:988 [job step2_2] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step2_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step2_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job step2_2] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step2_2] /private/tmp/docker_tmpptsgalmt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpptsgalmt,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp4qbnegg7,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmhfpqlte/20230605095045-609224.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step2_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step2_2] completed success\nDEBUG cwltool:job.py:422 [job step2_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpptsgalmt/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_2] produced output {}\nINFO cwltool:workflow_job.py:572 [step step2_2] completed success\nDEBUG cwltool:job.py:446 [job step2_2] Removing input staging directory /private/tmp/docker_tmpi7dfk_9x\nDEBUG cwltool:job.py:454 [job step2_2] Removing temporary directory /private/tmp/docker_tmp4qbnegg7\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgef2bfe92-5a62-4b36-b8ec-96b99ea4527f/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nERROR cwltool:workflow.py:465 Exception on step \'step1\'\nERROR cwltool:workflow_job.py:833 [step step1_2] Cannot make job: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 751, in try_make_job\n yield from jobs\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 77, in job\n yield from self.step.job(joborder, output_callback, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 459, in job\n yield from self.embedded_tool.job(\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 1090, in job\n adjustFileObjs(li, register_mut)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 273, in adjustFileObjs\n visit_class(rec, ("File",), op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 1080, in register_mut\n mm.register_mutation(j.name, f)\n File "/Users/jasperk/gitlab/cwltool/cwltool/mutation.py", line 69, in register_mutation\n raise WorkflowException(\ncwltool.errors.WorkflowException: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\nINFO cwltool:workflow_job.py:539 [workflow _2] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpptsgalmt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwij4jvx9\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.0014760510002815863, 'start': 1685951446.6416798, 'stop': 1685951446.6431592, '$report_type': 'TestReport', 'item_index': 374, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_write_write_conflict + location: ('tests/test_ext.py', 207, 'test_write_write_conflict') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_ext.py::test_read_write_conflict + location: ('tests/test_ext.py', 224, 'test_read_write_conflict') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_read_write_conflict', 'location': ('tests/test_ext.py', 224, 'test_read_write_conflict'), 'keywords': {'test_read_write_conflict': 1, 'skip': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_ext.py', 225, 'Skipped: This test is non-deterministic'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00024330199994437862, 'start': 1685951446.6445491, 'stop': 1685951446.644793, '$report_type': 'TestReport', 'item_index': 375, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_read_write_conflict', 'location': ('tests/test_ext.py', 224, 'test_read_write_conflict'), 'keywords': {'test_read_write_conflict': 1, 'skip': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0001879559995359159, 'start': 1685951446.64551, 'stop': 1685951446.645699, '$report_type': 'TestReport', 'item_index': 375, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_read_write_conflict + location: ('tests/test_ext.py', 224, 'test_read_write_conflict') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_require_prefix_networkaccess', 'location': ('tests/test_ext.py', 234, 'test_require_prefix_networkaccess'), 'keywords': {'test_require_prefix_networkaccess': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00022061199979361845, 'start': 1685951446.6465101, 'stop': 1685951446.646732, '$report_type': 'TestReport', 'item_index': 376, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_ext.py::test_require_prefix_networkaccess + location: ('tests/test_ext.py', 234, 'test_require_prefix_networkaccess') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters3-result3]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters3-result3]'), 'keywords': {'test_overrides[parameters3-result3]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters3-result3': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_5] /private/tmp/docker_tmp86l4ox2u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp86l4ox2u/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_5] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml",\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_5] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_5] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_5] /private/tmp/docker_tmp86l4ox2u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp86l4ox2u/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_5] outputs {\n "out": "zing hello4\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_5] Removing input staging directory /private/tmp/docker_tmp_n9ao4j7\nDEBUG cwltool:job.py:454 [job echo.cwl_5] Removing temporary directory /private/tmp/docker_tmpvsxoha6w\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp86l4ox2u\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.81195076899985, 'start': 1685951445.8809862, 'stop': 1685951446.692918, '$report_type': 'TestReport', 'item_index': 470, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters3-result3]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters3-result3]'), 'keywords': {'test_overrides[parameters3-result3]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters3-result3': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_5] /private/tmp/docker_tmp86l4ox2u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp86l4ox2u/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_5] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml",\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_5] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_5] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_5] /private/tmp/docker_tmp86l4ox2u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp86l4ox2u/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_5] outputs {\n "out": "zing hello4\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_5] Removing input staging directory /private/tmp/docker_tmp_n9ao4j7\nDEBUG cwltool:job.py:454 [job echo.cwl_5] Removing temporary directory /private/tmp/docker_tmpvsxoha6w\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp86l4ox2u\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000732627999241231, 'start': 1685951446.694444, 'stop': 1685951446.695177, '$report_type': 'TestReport', 'item_index': 470, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides[parameters3-result3] + location: ('tests/test_override.py', 76, 'test_overrides[parameters3-result3]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides[parameters4-result4] + location: ('tests/test_override.py', 76, 'test_overrides[parameters4-result4]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters4-result4]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters4-result4]'), 'keywords': {'test_overrides[parameters4-result4]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters4-result4': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000645279999844206, 'start': 1685951446.696661, 'stop': 1685951446.6973069, '$report_type': 'TestReport', 'item_index': 471, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable', 'location': ('tests/test_loop.py', 109, 'test_loop_single_variable'), 'keywords': {'test_loop_single_variable': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _13] start\n\x1b[1;30mINFO\x1b[0m [workflow _13] starting step subworkflow_2\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _13] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop.cwl:26:7: object id \'tests/loop/single-var-loop.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step subworkflow_2\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_2] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_2] inputs was {\n "i1": 10\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpyl41gacq\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0283650020001005, 'start': 1685951445.763399, 'stop': 1685951446.79174, '$report_type': 'TestReport', 'item_index': 428, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> +INFO 3.1 +INFO Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' +URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section? +tests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined +INFO [workflow _13] start +INFO [workflow _13] starting step subworkflow_2 +INFO [step subworkflow_2] start +INFO [step subworkflow_2] Iteration 1 completed success +INFO [step subworkflow_2] start +INFO [step subworkflow_2] Iteration 2 completed success +INFO [step subworkflow_2] start +INFO [step subworkflow_2] Iteration 3 completed success +INFO [step subworkflow_2] start +INFO [step subworkflow_2] Iteration 4 completed success +INFO [step subworkflow_2] start +INFO [step subworkflow_2] Iteration 5 completed success +INFO [step subworkflow_2] start +INFO [step subworkflow_2] Iteration 6 completed success +INFO [step subworkflow_2] start +INFO [step subworkflow_2] Iteration 7 completed success +INFO [step subworkflow_2] start +INFO [step subworkflow_2] Iteration 8 completed success +INFO [step subworkflow_2] start +INFO [step subworkflow_2] Iteration 9 completed success +INFO [step subworkflow_2] completed success +INFO [workflow _13] completed success +INFO Final process status is success +@PFNCaptured log callNyINFO cwltool:main.py:1027 3.1 +INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' +WARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section? +WARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined +DEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl +INFO cwltool:workflow_job.py:765 [workflow _13] start +DEBUG cwltool:workflow_job.py:777 [workflow _13] inputs { + "i1": 1 +} +INFO cwltool:workflow_job.py:613 [workflow _13] starting step subworkflow_2 +DEBUG cwltool:workflow_job.py:727 [step subworkflow_2] job input { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/i1": 1 +} +DEBUG cwltool:workflow_job.py:732 [step subworkflow_2] evaluated job input to { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/i1": 1 +} +INFO cwltool:workflow_job.py:75 [step subworkflow_2] start +DEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_2] produced output { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 2 +} +INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 1 completed success +INFO cwltool:workflow_job.py:75 [step subworkflow_2] start +DEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_2] produced output { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 3 +} +INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 2 completed success +INFO cwltool:workflow_job.py:75 [step subworkflow_2] start +DEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_2] produced output { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 4 +} +INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 3 completed success +INFO cwltool:workflow_job.py:75 [step subworkflow_2] start +DEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_2] produced output { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 5 +} +INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 4 completed success +INFO cwltool:workflow_job.py:75 [step subworkflow_2] start +DEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_2] produced output { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 6 +} +INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 5 completed success +INFO cwltool:workflow_job.py:75 [step subworkflow_2] start +DEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_2] produced output { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 7 +} +INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 6 completed success +INFO cwltool:workflow_job.py:75 [step subworkflow_2] start +DEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_2] produced output { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 8 +} +INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 7 completed success +INFO cwltool:workflow_job.py:75 [step subworkflow_2] start +DEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_2] produced output { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 9 +} +INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 8 completed success +INFO cwltool:workflow_job.py:75 [step subworkflow_2] start +DEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_2] produced output { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 10 +} +INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 9 completed success +DEBUG cwltool:workflow_job.py:918 [step subworkflow_2] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9 +DEBUG cwltool:workflow_job.py:925 [step subworkflow_2] inputs was { + "i1": 10 +} +DEBUG cwltool:workflow_job.py:564 [step subworkflow_2] produced output { + "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 10 +} +INFO cwltool:workflow_job.py:572 [step subworkflow_2] completed success +INFO cwltool:workflow_job.py:539 [workflow _13] completed success +DEBUG cwltool:workflow_job.py:541 [workflow _13] outputs { + "o1": 10 +} +DEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpyl41gacq +INFO cwltool:main.py:1366 Final process status is success@PPNdurationD?ðt.Ü?PNstartDAÙdõpÛ‡PNstopDAÙdõ²«ÞPN $report_typeN +TestReportPN +item_indexF¬PN worker_idNgw6PN testrun_uidN ca4970838f1b415dbaafd06f56809891PP@Qltool:job.py:419 [job count] completed success +DEBUG cwltool:job.py:422 [job count] outputs { + "line_count": { + "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count", + "basename": "line_count", + "nameroot": "line_count", + "nameext": "", + "class": "File", + "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbfÚK«Úÿÿÿÿÿÿÿä data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable', 'location': ('tests/test_loop.py', 109, 'test_loop_single_variable'), 'keywords': {'test_loop_single_variable': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-lo finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable_no_iteration', 'location': ('tests/test_loop.py', 122, 'test_loop_single_variable_no_iteration'), 'keywords': {'test_loop_single_variable_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00020065800072188722, 'start': 1685951446.793686, 'stop': 1685951446.793887, '$report_type': 'TestReport', 'item_index': 429, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_loop_single_variable + location: ('tests/test_loop.py', 109, 'test_loop_single_variable') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_loop_single_variable_no_iteration + location: ('tests/test_loop.py', 122, 'test_loop_single_variable_no_iteration') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_environment', 'location': ('tests/test_mpi.py', 194, 'TestMpiRun.test_environment'), 'keywords': {'test_environment': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job mpi_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_env.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_env.cwl] /private/tmp/docker_tmp156vbda6$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 1 \\\n --no-fail \\\n env > /private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_env.cwl] outputs {\n "environment": {\n "location": "file:///private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "basename": "fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "nameroot": "fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$0088a72a33becb2278fc4741a6d88339fd6f2210",\n "size": 1098,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_env.cwl] Removing input staging directory /private/tmp/docker_tmphcj1vukp\nDEBUG cwltool:job.py:454 [job mpi_env.cwl] Removing temporary directory /private/tmp/docker_tmpg8c5bbwz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_environment0/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp156vbda6\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9825167569997575, 'start': 1685951446.030616, 'stop': 1685951447.013109, '$report_type': 'TestReport', 'item_index': 459, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_environment', 'location': ('tests/test_mpi.py', 194, 'TestMpiRun.test_environment'), 'keywords': {'test_environment': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job mpi_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_env.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_env.cwl] /private/tmp/docker_tmp156vbda6$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 1 \\\n --no-fail \\\n env > /private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_env.cwl] outputs {\n "environment": {\n "location": "file:///private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "basename": "fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "nameroot": "fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$0088a72a33becb2278fc4741a6d88339fd6f2210",\n "size": 1098,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_env.cwl] Removing input staging directory /private/tmp/docker_tmphcj1vukp\nDEBUG cwltool:job.py:454 [job mpi_env.cwl] Removing temporary directory /private/tmp/docker_tmpg8c5bbwz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_environment0/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp156vbda6\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0016772190001574927, 'start': 1685951447.013999, 'stop': 1685951447.015678, '$report_type': 'TestReport', 'item_index': 459, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::TestMpiRun::test_environment + location: ('tests/test_mpi.py', 194, 'TestMpiRun.test_environment') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::test_env_passing + location: ('tests/test_mpi.py', 219, 'test_env_passing') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_env_passing', 'location': ('tests/test_mpi.py', 219, 'test_env_passing'), 'keywords': {'test_env_passing': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006188460001794738, 'start': 1685951447.017211, 'stop': 1685951447.0178308, '$report_type': 'TestReport', 'item_index': 460, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_env_passing', 'location': ('tests/test_mpi.py', 219, 'test_env_passing'), 'keywords': {'test_env_passing': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0007053230001474731, 'start': 1685951447.0186088, 'stop': 1685951447.019315, '$report_type': 'TestReport', 'item_index': 460, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_env_passing', 'location': ('tests/test_mpi.py', 219, 'test_env_passing'), 'keywords': {'test_env_passing': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000304819000120915, 'start': 1685951447.019708, 'stop': 1685951447.020014, '$report_type': 'TestReport', 'item_index': 460, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::test_env_passing + location: ('tests/test_mpi.py', 219, 'test_env_passing') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::test_singularity + location: ('tests/test_mpi.py', 317, 'test_singularity') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]'), 'keywords': {'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:46]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl'")], 'duration': 0.894511448999765, 'start': 1685951446.509061, 'stop': 1685951447.403552, '$report_type': 'TestReport', 'item_index': 481, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]'), 'keywords': {'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:46]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl'")], 'duration': 0.0004022650000479189, 'start': 1685951447.404211, 'stop': 1685951447.404615, '$report_type': 'TestReport', 'item_index': 481, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl] + location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl] + location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]'), 'keywords': {'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00043142699996678857, 'start': 1685951447.4058828, 'stop': 1685951447.406315, '$report_type': 'TestReport', 'item_index': 482, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]'), 'keywords': {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task2_12\nDEBUG cwltool:workflow_job.py:727 [step task2_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_12\nDEBUG cwltool:command_line_tool.py:988 [job task2_10] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_10] initial work dir {}\nINFO cwltool:job.py:266 [job task2_10] /private/tmp/docker_tmp2edpsbck$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2edpsbck,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwpqrjecs,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095045-366456.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_10] completed success\nDEBUG cwltool:job.py:422 [job task2_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2edpsbck/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_12] completed success\nDEBUG cwltool:job.py:446 [job task2_10] Removing input staging directory /private/tmp/docker_tmpparyqua4\nDEBUG cwltool:job.py:454 [job task2_10] Removing temporary directory /private/tmp/docker_tmpwpqrjecs\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task1_12\nDEBUG cwltool:workflow_job.py:727 [step task1_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_12\nDEBUG cwltool:command_line_tool.py:988 [job task1_10] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_10] initial work dir {}\nINFO cwltool:job.py:266 [job task1_10] /private/tmp/docker_tmpl6uhq9ur$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpl6uhq9ur,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp3v2v_ylx,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095046-398112.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_10] completed success\nDEBUG cwltool:job.py:422 [job task1_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpl6uhq9ur/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_12] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {}\nDEBUG cwltool:job.py:446 [job task1_10] Removing input staging directory /private/tmp/docker_tmp7cq588zt\nDEBUG cwltool:job.py:454 [job task1_10] Removing temporary directory /private/tmp/docker_tmp3v2v_ylx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmbshxay5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpl6uhq9ur\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2edpsbck\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 3.559965896999529, 'start': 1685951443.858878, 'stop': 1685951447.418756, '$report_type': 'TestReport', 'item_index': 278, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]'), 'keywords': {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task2_12\nDEBUG cwltool:workflow_job.py:727 [step task2_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_12\nDEBUG cwltool:command_line_tool.py:988 [job task2_10] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_10] initial work dir {}\nINFO cwltool:job.py:266 [job task2_10] /private/tmp/docker_tmp2edpsbck$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2edpsbck,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwpqrjecs,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095045-366456.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_10] completed success\nDEBUG cwltool:job.py:422 [job task2_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2edpsbck/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_12] completed success\nDEBUG cwltool:job.py:446 [job task2_10] Removing input staging directory /private/tmp/docker_tmpparyqua4\nDEBUG cwltool:job.py:454 [job task2_10] Removing temporary directory /private/tmp/docker_tmpwpqrjecs\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task1_12\nDEBUG cwltool:workflow_job.py:727 [step task1_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_12\nDEBUG cwltool:command_line_tool.py:988 [job task1_10] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_10] initial work dir {}\nINFO cwltool:job.py:266 [job task1_10] /private/tmp/docker_tmpl6uhq9ur$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpl6uhq9ur,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp3v2v_ylx,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095046-398112.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_10] completed success\nDEBUG cwltool:job.py:422 [job task1_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpl6uhq9ur/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_12] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {}\nDEBUG cwltool:job.py:446 [job task1_10] Removing input staging directory /private/tmp/docker_tmp7cq588zt\nDEBUG cwltool:job.py:454 [job task1_10] Removing temporary directory /private/tmp/docker_tmp3v2v_ylx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmbshxay5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpl6uhq9ur\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2edpsbck\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000630780999927083, 'start': 1685951447.419929, 'stop': 1685951447.4205608, '$report_type': 'TestReport', 'item_index': 278, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]'), 'keywords': {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0019516170004862943, 'start': 1685951447.422921, 'stop': 1685951447.424876, '$report_type': 'TestReport', 'item_index': 279, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters4-result4]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters4-result4]'), 'keywords': {'test_overrides[parameters4-result4]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters4-result4': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _14] start\n\x1b[1;30mINFO\x1b[0m [workflow _14] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmpnetcp5i3$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpnetcp5i3/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _14] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmpnetcp5i3$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpnetcp5i3/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello2\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpgmam1inb\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpno95obow\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnetcp5i3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptrv1sfqx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.733346445999814, 'start': 1685951446.697649, 'stop': 1685951447.430978, '$report_type': 'TestReport', 'item_index': 471, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters4-result4]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters4-result4]'), 'keywords': {'test_overrides[parameters4-result4]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters4-result4': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _14] start\n\x1b[1;30mINFO\x1b[0m [workflow _14] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmpnetcp5i3$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpnetcp5i3/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _14] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmpnetcp5i3$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpnetcp5i3/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello2\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpgmam1inb\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpno95obow\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnetcp5i3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptrv1sfqx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005950549993940513, 'start': 1685951447.432105, 'stop': 1685951447.4327009, '$report_type': 'TestReport', 'item_index': 471, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides[parameters4-result4] + location: ('tests/test_override.py', 76, 'test_overrides[parameters4-result4]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides[parameters5-result5] + location: ('tests/test_override.py', 76, 'test_overrides[parameters5-result5]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters5-result5]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters5-result5]'), 'keywords': {'test_overrides[parameters5-result5]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters5-result5': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005286280002110288, 'start': 1685951447.4340851, 'stop': 1685951447.434614, '$report_type': 'TestReport', 'item_index': 472, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]'), 'keywords': {'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl'")], 'duration': 0.10997923700051615, 'start': 1685951447.406658, 'stop': 1685951447.5166368, '$report_type': 'TestReport', 'item_index': 482, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]'), 'keywords': {'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl'")], 'duration': 0.00029306200030987384, 'start': 1685951447.517217, 'stop': 1685951447.517511, '$report_type': 'TestReport', 'item_index': 482, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl] + location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl] + location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]'), 'keywords': {'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00043338799969205866, 'start': 1685951447.518337, 'stop': 1685951447.518772, '$report_type': 'TestReport', 'item_index': 483, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]'), 'keywords': {'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl'\ntests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\ntests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl'\nWARNING salad:ref_resolver.py:1130 tests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\nWARNING salad:ref_resolver.py:1130 tests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined")], 'duration': 0.02941035300045769, 'start': 1685951447.5191061, 'stop': 1685951447.548518, '$report_type': 'TestReport', 'item_index': 483, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]'), 'keywords': {'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl'\ntests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\ntests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl'\nWARNING salad:ref_resolver.py:1130 tests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\nWARNING salad:ref_resolver.py:1130 tests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined")], 'duration': 0.00037038899972685613, 'start': 1685951447.549118, 'stop': 1685951447.54949, '$report_type': 'TestReport', 'item_index': 483, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl] + location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl] + location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005589559996224125, 'start': 1685951447.550621, 'stop': 1685951447.551181, '$report_type': 'TestReport', 'item_index': 484, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable_no_iteration', 'location': ('tests/test_loop.py', 122, 'test_loop_single_variable_no_iteration'), 'keywords': {'test_loop_single_variable_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/single-var-loop-no-iteration.cwl:26:7: object id 'tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _14] start\n\x1b[1;30mINFO\x1b[0m [workflow _14] starting step subworkflow_3\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _14] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop-no-iteration.cwl:26:7: object id \'tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step subworkflow_3\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_3] loop condition $(inputs.i1 < 1) evaluated to False at iteration 0\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_3] inputs was {\n "i1": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_3] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "o1": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpypaeahap\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.970427149999523, 'start': 1685951446.7942111, 'stop': 1685951447.7646148, '$report_type': 'TestReport', 'item_index': 429, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable_no_iteration', 'location': ('tests/test_loop.py', 122, 'test_loop_single_variable_no_iteration'), 'keywords': {'test_loop_single_variable_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/single-var-loop-no-iteration.cwl:26:7: object id 'tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _14] start\n\x1b[1;30mINFO\x1b[0m [workflow _14] starting step subworkflow_3\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _14] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop-no-iteration.cwl:26:7: object id \'tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step subworkflow_3\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_3] loop condition $(inputs.i1 < 1) evaluated to False at iteration 0\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_3] inputs was {\n "i1": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_3] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "o1": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpypaeahap\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0003115270001217141, 'start': 1685951447.765162, 'stop': 1685951447.765474, '$report_type': 'TestReport', 'item_index': 429, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables', 'location': ('tests/test_loop.py', 135, 'test_loop_two_variables'), 'keywords': {'test_loop_two_variables': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002811579997796798, 'start': 1685951447.766572, 'stop': 1685951447.7668538, '$report_type': 'TestReport', 'item_index': 430, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_loop_single_variable_no_iteration + location: ('tests/test_loop.py', 122, 'test_loop_single_variable_no_iteration') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_loop_two_variables + location: ('tests/test_loop.py', 135, 'test_loop_two_variables') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_singularity', 'location': ('tests/test_mpi.py', 317, 'test_singularity'), 'keywords': {'test_singularity': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.7677750800003196, 'start': 1685951447.021031, 'stop': 1685951447.788788, '$report_type': 'TestReport', 'item_index': 461, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_singularity', 'location': ('tests/test_mpi.py', 317, 'test_singularity'), 'keywords': {'test_singularity': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.007320910999624175, 'start': 1685951447.789354, 'stop': 1685951447.7966762, '$report_type': 'TestReport', 'item_index': 461, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_singularity', 'location': ('tests/test_mpi.py', 317, 'test_singularity'), 'keywords': {'test_singularity': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.00023004299964668462, 'start': 1685951447.7974741, 'stop': 1685951447.797705, '$report_type': 'TestReport', 'item_index': 461, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::test_singularity + location: ('tests/test_mpi.py', 317, 'test_singularity') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_udocker', 'location': ('tests/test_mpi.py', 324, 'test_udocker'), 'keywords': {'test_udocker': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003294099997219746, 'start': 1685951447.7988281, 'stop': 1685951447.799159, '$report_type': 'TestReport', 'item_index': 462, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::test_udocker + location: ('tests/test_mpi.py', 324, 'test_udocker') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_udocker', 'location': ('tests/test_mpi.py', 324, 'test_udocker'), 'keywords': {'test_udocker': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.008525170999746479, 'start': 1685951447.799621, 'stop': 1685951447.808148, '$report_type': 'TestReport', 'item_index': 462, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_udocker', 'location': ('tests/test_mpi.py', 324, 'test_udocker'), 'keywords': {'test_udocker': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.0002947040002254653, 'start': 1685951447.808861, 'stop': 1685951447.8091571, '$report_type': 'TestReport', 'item_index': 462, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::test_udocker + location: ('tests/test_mpi.py', 324, 'test_udocker') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::test_docker_hint + location: ('tests/test_mpi.py', 331, 'test_docker_hint') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_hint', 'location': ('tests/test_mpi.py', 331, 'test_docker_hint'), 'keywords': {'test_docker_hint': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00025352200009365333, 'start': 1685951447.8103979, 'stop': 1685951447.810652, '$report_type': 'TestReport', 'item_index': 463, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_hint', 'location': ('tests/test_mpi.py', 331, 'test_docker_hint'), 'keywords': {'test_docker_hint': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint DockerRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPI has been required while Docker is hinted, discarding Docker hint(s)\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint DockerRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature\nWARNING cwltool:command_line_tool.py:453 MPI has been required while Docker is hinted, discarding Docker hint(s)')], 'duration': 0.007302015000277606, 'start': 1685951447.81097, 'stop': 1685951447.818273, '$report_type': 'TestReport', 'item_index': 463, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_hint', 'location': ('tests/test_mpi.py', 331, 'test_docker_hint'), 'keywords': {'test_docker_hint': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint DockerRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPI has been required while Docker is hinted, discarding Docker hint(s)\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint DockerRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature\nWARNING cwltool:command_line_tool.py:453 MPI has been required while Docker is hinted, discarding Docker hint(s)')], 'duration': 0.0002557699999670149, 'start': 1685951447.8188071, 'stop': 1685951447.819063, '$report_type': 'TestReport', 'item_index': 463, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::test_docker_hint + location: ('tests/test_mpi.py', 331, 'test_docker_hint') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::test_docker_required + location: ('tests/test_mpi.py', 339, 'test_docker_required') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_required', 'location': ('tests/test_mpi.py', 339, 'test_docker_required'), 'keywords': {'test_docker_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003120929995930055, 'start': 1685951447.820271, 'stop': 1685951447.8205838, '$report_type': 'TestReport', 'item_index': 464, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_required', 'location': ('tests/test_mpi.py', 339, 'test_docker_required'), 'keywords': {'test_docker_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint http://commonwl.org/cwltool#MPIRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mDocker has been required while MPI is hinted, discarding MPI hint(s)\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint http://commonwl.org/cwltool#MPIRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature\nWARNING cwltool:command_line_tool.py:460 Docker has been required while MPI is hinted, discarding MPI hint(s)')], 'duration': 0.008689338999829488, 'start': 1685951447.821028, 'stop': 1685951447.829718, '$report_type': 'TestReport', 'item_index': 464, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_required', 'location': ('tests/test_mpi.py', 339, 'test_docker_required'), 'keywords': {'test_docker_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint http://commonwl.org/cwltool#MPIRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mDocker has been required while MPI is hinted, discarding MPI hint(s)\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint http://commonwl.org/cwltool#MPIRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature\nWARNING cwltool:command_line_tool.py:460 Docker has been required while MPI is hinted, discarding MPI hint(s)')], 'duration': 0.00021788699996250216, 'start': 1685951447.830179, 'stop': 1685951447.8303978, '$report_type': 'TestReport', 'item_index': 464, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_required', 'location': ('tests/test_mpi.py', 347, 'test_docker_mpi_both_required'), 'keywords': {'test_docker_mpi_both_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00027876399963133736, 'start': 1685951447.831475, 'stop': 1685951447.831756, '$report_type': 'TestReport', 'item_index': 465, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::test_docker_required + location: ('tests/test_mpi.py', 339, 'test_docker_required') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::test_docker_mpi_both_required + location: ('tests/test_mpi.py', 347, 'test_docker_mpi_both_required') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_required', 'location': ('tests/test_mpi.py', 347, 'test_docker_mpi_both_required'), 'keywords': {'test_docker_mpi_both_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', " \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\nreceived command runtests {'indices': [513, 514, 515, 516, 517, 518]}"), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.008565494999857037, 'start': 1685951447.832157, 'stop': 1685951447.840724, '$report_type': 'TestReport', 'item_index': 465, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_required', 'location': ('tests/test_mpi.py', 347, 'test_docker_mpi_both_required'), 'keywords': {'test_docker_mpi_both_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', " \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\nreceived command runtests {'indices': [513, 514, 515, 516, 517, 518]}"), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature'), ('Captured stderr teardown', '\n')], 'duration': 0.0002890880004997598, 'start': 1685951447.84132, 'stop': 1685951447.84161, '$report_type': 'TestReport', 'item_index': 465, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::test_docker_mpi_both_required + location: ('tests/test_mpi.py', 347, 'test_docker_mpi_both_required') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_mpi.py::test_docker_mpi_both_hinted + location: ('tests/test_mpi.py', 355, 'test_docker_mpi_both_hinted') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_hinted', 'location': ('tests/test_mpi.py', 355, 'test_docker_mpi_both_hinted'), 'keywords': {'test_docker_mpi_both_hinted': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003151740002067527, 'start': 1685951447.842783, 'stop': 1685951447.8430998, '$report_type': 'TestReport', 'item_index': 466, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_hinted', 'location': ('tests/test_mpi.py', 355, 'test_docker_mpi_both_hinted'), 'keywords': {'test_docker_mpi_both_hinted': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint http://commonwl.org/cwltool#MPIRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint DockerRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint http://commonwl.org/cwltool#MPIRequirement\nINFO cwltool:process.py:1070 Unknown hint DockerRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.06096013200021844, 'start': 1685951447.843498, 'stop': 1685951447.904458, '$report_type': 'TestReport', 'item_index': 466, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_hinted', 'location': ('tests/test_mpi.py', 355, 'test_docker_mpi_both_hinted'), 'keywords': {'test_docker_mpi_both_hinted': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint http://commonwl.org/cwltool#MPIRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint DockerRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint http://commonwl.org/cwltool#MPIRequirement\nINFO cwltool:process.py:1070 Unknown hint DockerRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.00019882299966411665, 'start': 1685951447.904893, 'stop': 1685951447.9050932, '$report_type': 'TestReport', 'item_index': 466, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_mpi.py::test_docker_mpi_both_hinted + location: ('tests/test_mpi.py', 355, 'test_docker_mpi_both_hinted') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides[parameters0-result0] + location: ('tests/test_override.py', 76, 'test_overrides[parameters0-result0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters0-result0]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters0-result0]'), 'keywords': {'test_overrides[parameters0-result0]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-result0': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009969010006898316, 'start': 1685951447.906661, 'stop': 1685951447.907661, '$report_type': 'TestReport', 'item_index': 467, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters5-result5]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters5-result5]'), 'keywords': {'test_overrides[parameters5-result5]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters5-result5': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpj04h1f3l$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpj04h1f3l/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpj04h1f3l$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpj04h1f3l/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "out": "zing hello5\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello5\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": "zing hello5\\n"\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpvw9dygow\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpe804kt2a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvimgwujy\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj04h1f3l\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7897590640004637, 'start': 1685951447.434944, 'stop': 1685951448.224685, '$report_type': 'TestReport', 'item_index': 472, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters5-result5]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters5-result5]'), 'keywords': {'test_overrides[parameters5-result5]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters5-result5': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpj04h1f3l$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpj04h1f3l/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpj04h1f3l$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpj04h1f3l/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "out": "zing hello5\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello5\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": "zing hello5\\n"\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpvw9dygow\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpe804kt2a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvimgwujy\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj04h1f3l\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007478079996872111, 'start': 1685951448.2257411, 'stop': 1685951448.22649, '$report_type': 'TestReport', 'item_index': 472, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides[parameters5-result5] + location: ('tests/test_override.py', 76, 'test_overrides[parameters5-result5]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides[parameters6-result6] + location: ('tests/test_override.py', 76, 'test_overrides[parameters6-result6]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters6-result6]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters6-result6]'), 'keywords': {'test_overrides[parameters6-result6]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters6-result6': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009183920001305523, 'start': 1685951448.228301, 'stop': 1685951448.2292202, '$report_type': 'TestReport', 'item_index': 473, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters0-result0]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters0-result0]'), 'keywords': {'test_overrides[parameters0-result0]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-result0': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_2] /private/tmp/docker_tmpfp0t3l3u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpfp0t3l3u/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_2] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_2] /private/tmp/docker_tmpfp0t3l3u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpfp0t3l3u/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_2] outputs {\n "out": "zing hello1\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_2] Removing input staging directory /private/tmp/docker_tmpeqs91hzx\nDEBUG cwltool:job.py:454 [job echo.cwl_2] Removing temporary directory /private/tmp/docker_tmp40o02aoz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfp0t3l3u\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.730464029000359, 'start': 1685951447.908118, 'stop': 1685951448.638567, '$report_type': 'TestReport', 'item_index': 467, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters0-result0]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters0-result0]'), 'keywords': {'test_overrides[parameters0-result0]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-result0': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_2] /private/tmp/docker_tmpfp0t3l3u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpfp0t3l3u/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_2] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_2] /private/tmp/docker_tmpfp0t3l3u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpfp0t3l3u/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_2] outputs {\n "out": "zing hello1\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_2] Removing input staging directory /private/tmp/docker_tmpeqs91hzx\nDEBUG cwltool:job.py:454 [job echo.cwl_2] Removing temporary directory /private/tmp/docker_tmp40o02aoz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfp0t3l3u\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.001413670000147249, 'start': 1685951448.6403031, 'stop': 1685951448.641719, '$report_type': 'TestReport', 'item_index': 467, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides[parameters0-result0] + location: ('tests/test_override.py', 76, 'test_overrides[parameters0-result0]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pathmapper.py::test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0] + location: ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]'), 'keywords': {'test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]': 1, 'parametrize': 1, 'pytestmark': 1, 'strip trailing slashes-file_dir0-expected0': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001069932000064, 'start': 1685951448.644154, 'stop': 1685951448.645225, '$report_type': 'TestReport', 'item_index': 513, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]'), 'keywords': {'test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]': 1, 'parametrize': 1, 'pytestmark': 1, 'strip trailing slashes-file_dir0-expected0': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00043503899996721884, 'start': 1685951448.645837, 'stop': 1685951448.6462731, '$report_type': 'TestReport', 'item_index': 513, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]'), 'keywords': {'test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]': 1, 'parametrize': 1, 'pytestmark': 1, 'strip trailing slashes-file_dir0-expected0': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005063790003987378, 'start': 1685951448.646919, 'stop': 1685951448.647427, '$report_type': 'TestReport', 'item_index': 513, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pathmapper.py::test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0] + location: ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pathmapper.py::test_normalizeFilesDirs[file-file_dir1-expected1] + location: ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file-file_dir1-expected1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file-file_dir1-expected1]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file-file_dir1-expected1]'), 'keywords': {'test_normalizeFilesDirs[file-file_dir1-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, 'file-file_dir1-expected1': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008652080005049356, 'start': 1685951448.649068, 'stop': 1685951448.649935, '$report_type': 'TestReport', 'item_index': 514, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file-file_dir1-expected1]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file-file_dir1-expected1]'), 'keywords': {'test_normalizeFilesDirs[file-file_dir1-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, 'file-file_dir1-expected1': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004152450001129182, 'start': 1685951448.650466, 'stop': 1685951448.650882, '$report_type': 'TestReport', 'item_index': 514, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file-file_dir1-expected1]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file-file_dir1-expected1]'), 'keywords': {'test_normalizeFilesDirs[file-file_dir1-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, 'file-file_dir1-expected1': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00046641399967484176, 'start': 1685951448.651627, 'stop': 1685951448.652096, '$report_type': 'TestReport', 'item_index': 514, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pathmapper.py::test_normalizeFilesDirs[file-file_dir1-expected1] + location: ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file-file_dir1-expected1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pathmapper.py::test_normalizeFilesDirs[file with local uri-file_dir2-expected2] + location: ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with local uri-file_dir2-expected2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file with local uri-file_dir2-expected2]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with local uri-file_dir2-expected2]'), 'keywords': {'test_normalizeFilesDirs[file with local uri-file_dir2-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, 'file with local uri-file_dir2-expected2': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008206479997170391, 'start': 1685951448.6534479, 'stop': 1685951448.65427, '$report_type': 'TestReport', 'item_index': 515, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file with local uri-file_dir2-expected2]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with local uri-file_dir2-expected2]'), 'keywords': {'test_normalizeFilesDirs[file with local uri-file_dir2-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, 'file with local uri-file_dir2-expected2': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005807630004710518, 'start': 1685951448.654985, 'stop': 1685951448.655568, '$report_type': 'TestReport', 'item_index': 515, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file with local uri-file_dir2-expected2]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with local uri-file_dir2-expected2]'), 'keywords': {'test_normalizeFilesDirs[file with local uri-file_dir2-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, 'file with local uri-file_dir2-expected2': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005976080001346418, 'start': 1685951448.656239, 'stop': 1685951448.656839, '$report_type': 'TestReport', 'item_index': 515, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pathmapper.py::test_normalizeFilesDirs[file with local uri-file_dir2-expected2] + location: ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with local uri-file_dir2-expected2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pathmapper.py::test_normalizeFilesDirs[file with http url-file_dir3-expected3] + location: ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with http url-file_dir3-expected3]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file with http url-file_dir3-expected3]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with http url-file_dir3-expected3]'), 'keywords': {'test_normalizeFilesDirs[file with http url-file_dir3-expected3]': 1, 'parametrize': 1, 'pytestmark': 1, 'file with http url-file_dir3-expected3': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001273665000553592, 'start': 1685951448.658586, 'stop': 1685951448.659861, '$report_type': 'TestReport', 'item_index': 516, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file with http url-file_dir3-expected3]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with http url-file_dir3-expected3]'), 'keywords': {'test_normalizeFilesDirs[file with http url-file_dir3-expected3]': 1, 'parametrize': 1, 'pytestmark': 1, 'file with http url-file_dir3-expected3': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x00runtests {'indices': [519, 520, 521, 522, 523, 524]}\n")], 'duration': 0.0006768519997422118, 'start': 1685951448.6603231, 'stop': 1685951448.661001, '$report_type': 'TestReport', 'item_index': 516, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file with http url-file_dir3-expected3]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with http url-file_dir3-expected3]'), 'keywords': {'test_normalizeFilesDirs[file with http url-file_dir3-expected3]': 1, 'parametrize': 1, 'pytestmark': 1, 'file with http url-file_dir3-expected3': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x00runtests {'indices': [519, 520, 521, 522, 523, 524]}\n")], 'duration': 0.00040179000006901333, 'start': 1685951448.6614861, 'stop': 1685951448.661889, '$report_type': 'TestReport', 'item_index': 516, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pathmapper.py::test_normalizeFilesDirs[file with http url-file_dir3-expected3] + location: ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with http url-file_dir3-expected3]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pathmapper.py::test_basename_field_generation[foo.bar-expected0] + location: ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.bar-expected0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo.bar-expected0]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.bar-expected0]'), 'keywords': {'test_basename_field_generation[foo.bar-expected0]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar-expected0': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00047172599988698494, 'start': 1685951448.6631749, 'stop': 1685951448.663648, '$report_type': 'TestReport', 'item_index': 517, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo.bar-expected0]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.bar-expected0]'), 'keywords': {'test_basename_field_generation[foo.bar-expected0]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar-expected0': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000560776999918744, 'start': 1685951448.664203, 'stop': 1685951448.664765, '$report_type': 'TestReport', 'item_index': 517, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo.bar-expected0]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.bar-expected0]'), 'keywords': {'test_basename_field_generation[foo.bar-expected0]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar-expected0': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00034523100021033315, 'start': 1685951448.665802, 'stop': 1685951448.6661491, '$report_type': 'TestReport', 'item_index': 517, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pathmapper.py::test_basename_field_generation[foo.bar-expected0] + location: ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.bar-expected0]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pathmapper.py::test_basename_field_generation[foo-expected1] + location: ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo-expected1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo-expected1]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo-expected1]'), 'keywords': {'test_basename_field_generation[foo-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo-expected1': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005737189994761138, 'start': 1685951448.667606, 'stop': 1685951448.668181, '$report_type': 'TestReport', 'item_index': 518, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo-expected1]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo-expected1]'), 'keywords': {'test_basename_field_generation[foo-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo-expected1': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00029892800012021326, 'start': 1685951448.668575, 'stop': 1685951448.668876, '$report_type': 'TestReport', 'item_index': 518, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo-expected1]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo-expected1]'), 'keywords': {'test_basename_field_generation[foo-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo-expected1': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003486380001049838, 'start': 1685951448.669343, 'stop': 1685951448.669693, '$report_type': 'TestReport', 'item_index': 518, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pathmapper.py::test_basename_field_generation[foo-expected1] + location: ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo-expected1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pathmapper.py::test_basename_field_generation[.foo-expected2] + location: ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[.foo-expected2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[.foo-expected2]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[.foo-expected2]'), 'keywords': {'test_basename_field_generation[.foo-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, '.foo-expected2': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005889219992241124, 'start': 1685951448.670938, 'stop': 1685951448.6715279, '$report_type': 'TestReport', 'item_index': 519, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[.foo-expected2]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[.foo-expected2]'), 'keywords': {'test_basename_field_generation[.foo-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, '.foo-expected2': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004950350003127824, 'start': 1685951448.671987, 'stop': 1685951448.672485, '$report_type': 'TestReport', 'item_index': 519, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[.foo-expected2]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[.foo-expected2]'), 'keywords': {'test_basename_field_generation[.foo-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, '.foo-expected2': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007235059993035975, 'start': 1685951448.673044, 'stop': 1685951448.67377, '$report_type': 'TestReport', 'item_index': 519, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pathmapper.py::test_basename_field_generation[.foo-expected2] + location: ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[.foo-expected2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pathmapper.py::test_basename_field_generation[foo.-expected3] + location: ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.-expected3]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo.-expected3]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.-expected3]'), 'keywords': {'test_basename_field_generation[foo.-expected3]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.-expected3': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005656649991578888, 'start': 1685951448.6750562, 'stop': 1685951448.675624, '$report_type': 'TestReport', 'item_index': 520, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo.-expected3]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.-expected3]'), 'keywords': {'test_basename_field_generation[foo.-expected3]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.-expected3': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00039465200006816303, 'start': 1685951448.676179, 'stop': 1685951448.676575, '$report_type': 'TestReport', 'item_index': 520, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo.-expected3]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.-expected3]'), 'keywords': {'test_basename_field_generation[foo.-expected3]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.-expected3': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007300159995793365, 'start': 1685951448.677197, 'stop': 1685951448.677928, '$report_type': 'TestReport', 'item_index': 520, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pathmapper.py::test_basename_field_generation[foo.-expected3] + location: ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.-expected3]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pathmapper.py::test_basename_field_generation[foo.bar.baz-expected4] + location: ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.bar.baz-expected4]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo.bar.baz-expected4]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.bar.baz-expected4]'), 'keywords': {'test_basename_field_generation[foo.bar.baz-expected4]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar.baz-expected4': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006587759999092668, 'start': 1685951448.6791732, 'stop': 1685951448.6798332, '$report_type': 'TestReport', 'item_index': 521, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo.bar.baz-expected4]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.bar.baz-expected4]'), 'keywords': {'test_basename_field_generation[foo.bar.baz-expected4]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar.baz-expected4': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004871339997407631, 'start': 1685951448.6804638, 'stop': 1685951448.680953, '$report_type': 'TestReport', 'item_index': 521, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo.bar.baz-expected4]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.bar.baz-expected4]'), 'keywords': {'test_basename_field_generation[foo.bar.baz-expected4]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar.baz-expected4': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000340042999596335, 'start': 1685951448.6817448, 'stop': 1685951448.682087, '$report_type': 'TestReport', 'item_index': 521, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pathmapper.py::test_basename_field_generation[foo.bar.baz-expected4] + location: ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.bar.baz-expected4]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_procgenerator.py::test_missing_enable_ext + location: ('tests/test_procgenerator.py', 11, 'test_missing_enable_ext') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_procgenerator.py::test_missing_enable_ext', 'location': ('tests/test_procgenerator.py', 11, 'test_missing_enable_ext'), 'keywords': {'test_missing_enable_ext': 1, 'test_procgenerator.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw5] received command runtests {'indices': [525, 526, 527, 528, 529]}\n")], 'duration': 0.0021776809999209945, 'start': 1685951448.683458, 'stop': 1685951448.6856372, '$report_type': 'TestReport', 'item_index': 522, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables', 'location': ('tests/test_loop.py', 135, 'test_loop_two_variables'), 'keywords': {'test_loop_two_variables': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/two-vars-loop.cwl:28:7: object id 'tests/loop/two-vars-loop.cwl#subworkflow/i1' previously defined\ntests/loop/two-vars-loop.cwl:29:7: object id 'tests/loop/two-vars-loop.cwl#subworkflow/i2' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step subworkflow_4\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop.cwl:28:7: object id \'tests/loop/two-vars-loop.cwl#subworkflow/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop.cwl:29:7: object id \'tests/loop/two-vars-loop.cwl#subworkflow/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step subworkflow_4\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 6,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 7,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 8,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 9,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 10,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_4] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_4] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 10,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpb71y25y0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0642764849999367, 'start': 1685951447.7672498, 'stop': 1685951448.831501, '$report_type': 'TestReport', 'item_index': 430, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables', 'location': ('tests/test_loop.py', 135, 'test_loop_two_variables'), 'keywords': {'test_loop_two_variables': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/two-vars-loop.cwl:28:7: object id 'tests/loop/two-vars-loop.cwl#subworkflow/i1' previously defined\ntests/loop/two-vars-loop.cwl:29:7: object id 'tests/loop/two-vars-loop.cwl#subworkflow/i2' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step subworkflow_4\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop.cwl:28:7: object id \'tests/loop/two-vars-loop.cwl#subworkflow/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop.cwl:29:7: object id \'tests/loop/two-vars-loop.cwl#subworkflow/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step subworkflow_4\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 6,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 7,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 8,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 9,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 10,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_4] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_4] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 10,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpb71y25y0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00027263499941909686, 'start': 1685951448.8321788, 'stop': 1685951448.832453, '$report_type': 'TestReport', 'item_index': 430, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_loop_two_variables + location: ('tests/test_loop.py', 135, 'test_loop_two_variables') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_loop.py::test_loop_two_variables_single_backpropagation + location: ('tests/test_loop.py', 148, 'test_loop_two_variables_single_backpropagation') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables_single_backpropagation', 'location': ('tests/test_loop.py', 148, 'test_loop_two_variables_single_backpropagation'), 'keywords': {'test_loop_two_variables_single_backpropagation': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00021312199987733038, 'start': 1685951448.8346372, 'stop': 1685951448.834851, '$report_type': 'TestReport', 'item_index': 431, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters6-result6]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters6-result6]'), 'keywords': {'test_overrides[parameters6-result6]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters6-result6': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_3] /private/tmp/docker_tmpom9d8ntn$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpom9d8ntn/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpom9d8ntn$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpom9d8ntn/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": "zing hello6\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello6\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "out": "zing hello6\\n"\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfoeamufx\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmpt43592ho\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpom9d8ntn\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpacyeypq2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9073105670004225, 'start': 1685951448.2299478, 'stop': 1685951449.137239, '$report_type': 'TestReport', 'item_index': 473, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters6-result6]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters6-result6]'), 'keywords': {'test_overrides[parameters6-result6]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters6-result6': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_3] /private/tmp/docker_tmpom9d8ntn$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpom9d8ntn/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpom9d8ntn$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpom9d8ntn/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": "zing hello6\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello6\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "out": "zing hello6\\n"\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfoeamufx\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmpt43592ho\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpom9d8ntn\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpacyeypq2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006992500002525048, 'start': 1685951449.138462, 'stop': 1685951449.1391628, '$report_type': 'TestReport', 'item_index': 473, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides[parameters6-result6] + location: ('tests/test_override.py', 76, 'test_overrides[parameters6-result6]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides[parameters7-result7] + location: ('tests/test_override.py', 76, 'test_overrides[parameters7-result7]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters7-result7]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters7-result7]'), 'keywords': {'test_overrides[parameters7-result7]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters7-result7': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009293820003222208, 'start': 1685951449.141689, 'stop': 1685951449.1426198, '$report_type': 'TestReport', 'item_index': 474, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]'), 'keywords': {'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:45]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[1;30mINFO\x1b[0m [workflow _3] start\n\x1b[1;30mINFO\x1b[0m [workflow _3] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmp26s71h5c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp26s71h5c,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpol7xhy3g,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp_0898t8u/20230605095045-906739.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt > /private/tmp/docker_tmp26s71h5c/output\n\x1b[1;30mINFO\x1b[0m [job step1] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _3] starting step step2\n\x1b[1;30mINFO\x1b[0m [step step2] start\n\x1b[1;30mINFO\x1b[0m [step step2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _3] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] initialized from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] starting step step1_2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#wc-tool.cwl as part of step step1_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] initial work dir {}\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1_2] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmp77etqg31$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp77etqg31,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp69rybhp1,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp7z_ke77g/20230605095048-545487.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt > /private/tmp/docker_tmp77etqg31/output\n\x1b[1;30mINFO\x1b[0m [job step1_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] Removing input staging directory /private/tmp/docker_tmpt4xj39bu\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] Removing temporary directory /private/tmp/docker_tmp69rybhp1\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] starting step step2_2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_2] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/output": 16\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] outputs {\n "count_output": 16\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpfdsc75o7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp77etqg31\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp26s71h5c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp26s71h5c,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpol7xhy3g,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp_0898t8u/20230605095045-906739.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt > /private/tmp/docker_tmp26s71h5c/output\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpl05vyv1q\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpol7xhy3g\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step2\nDEBUG cwltool:workflow_job.py:727 [step step2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2] start\nDEBUG cwltool:workflow_job.py:564 [step step2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppuyriqxl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp26s71h5c\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\'\nDEBUG cwltool:workflow_job.py:498 [workflow _4] initialized from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main\nINFO cwltool:workflow_job.py:765 [workflow _4] start\nDEBUG cwltool:workflow_job.py:777 [workflow _4] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _4] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#wc-tool.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1_2] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmp77etqg31$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp77etqg31,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp69rybhp1,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp7z_ke77g/20230605095048-545487.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt > /private/tmp/docker_tmp77etqg31/output\nINFO cwltool:job.py:905 [job step1_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpt4xj39bu\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmp69rybhp1\nINFO cwltool:workflow_job.py:613 [workflow _4] starting step step2_2\nDEBUG cwltool:workflow_job.py:727 [step step2_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_2] start\nDEBUG cwltool:workflow_job.py:564 [step step2_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _4] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfdsc75o7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp77etqg31\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 4.536852426000223, 'start': 1685951445.0456069, 'stop': 1685951449.582348, '$report_type': 'TestReport', 'item_index': 492, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]'), 'keywords': {'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:45]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[1;30mINFO\x1b[0m [workflow _3] start\n\x1b[1;30mINFO\x1b[0m [workflow _3] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmp26s71h5c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp26s71h5c,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpol7xhy3g,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp_0898t8u/20230605095045-906739.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt > /private/tmp/docker_tmp26s71h5c/output\n\x1b[1;30mINFO\x1b[0m [job step1] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _3] starting step step2\n\x1b[1;30mINFO\x1b[0m [step step2] start\n\x1b[1;30mINFO\x1b[0m [step step2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _3] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] initialized from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] starting step step1_2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#wc-tool.cwl as part of step step1_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] initial work dir {}\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1_2] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmp77etqg31$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp77etqg31,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp69rybhp1,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp7z_ke77g/20230605095048-545487.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt > /private/tmp/docker_tmp77etqg31/output\n\x1b[1;30mINFO\x1b[0m [job step1_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] Removing input staging directory /private/tmp/docker_tmpt4xj39bu\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] Removing temporary directory /private/tmp/docker_tmp69rybhp1\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] starting step step2_2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_2] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/output": 16\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] outputs {\n "count_output": 16\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpfdsc75o7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp77etqg31\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp26s71h5c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp26s71h5c,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpol7xhy3g,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp_0898t8u/20230605095045-906739.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt > /private/tmp/docker_tmp26s71h5c/output\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpl05vyv1q\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpol7xhy3g\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step2\nDEBUG cwltool:workflow_job.py:727 [step step2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2] start\nDEBUG cwltool:workflow_job.py:564 [step step2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppuyriqxl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp26s71h5c\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\'\nDEBUG cwltool:workflow_job.py:498 [workflow _4] initialized from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main\nINFO cwltool:workflow_job.py:765 [workflow _4] start\nDEBUG cwltool:workflow_job.py:777 [workflow _4] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _4] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#wc-tool.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1_2] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmp77etqg31$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp77etqg31,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp69rybhp1,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp7z_ke77g/20230605095048-545487.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt > /private/tmp/docker_tmp77etqg31/output\nINFO cwltool:job.py:905 [job step1_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpt4xj39bu\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmp69rybhp1\nINFO cwltool:workflow_job.py:613 [workflow _4] starting step step2_2\nDEBUG cwltool:workflow_job.py:727 [step step2_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_2] start\nDEBUG cwltool:workflow_job.py:564 [step step2_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _4] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfdsc75o7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp77etqg31\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0011825430001408677, 'start': 1685951449.584609, 'stop': 1685951449.585794, '$report_type': 'TestReport', 'item_index': 492, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False] + location: ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True] + location: ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]'), 'keywords': {'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/formattest.cwl-tests/wf/formattest-job.json-True': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.002233817000160343, 'start': 1685951449.588507, 'stop': 1685951449.590742, '$report_type': 'TestReport', 'item_index': 493, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables_single_backpropagation', 'location': ('tests/test_loop.py', 148, 'test_loop_two_variables_single_backpropagation'), 'keywords': {'test_loop_two_variables_single_backpropagation': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/two-vars-loop-2.cwl:27:7: object id 'tests/loop/two-vars-loop-2.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step subworkflow_5\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop-2.cwl:27:7: object id \'tests/loop/two-vars-loop-2.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step subworkflow_5\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_5] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_5] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5pf69jm7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0921014760006074, 'start': 1685951448.835296, 'stop': 1685951449.927371, '$report_type': 'TestReport', 'item_index': 431, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables_single_backpropagation', 'location': ('tests/test_loop.py', 148, 'test_loop_two_variables_single_backpropagation'), 'keywords': {'test_loop_two_variables_single_backpropagation': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/two-vars-loop-2.cwl:27:7: object id 'tests/loop/two-vars-loop-2.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step subworkflow_5\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop-2.cwl:27:7: object id \'tests/loop/two-vars-loop-2.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step subworkflow_5\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_5] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_5] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5pf69jm7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00025226599973393604, 'start': 1685951449.9279418, 'stop': 1685951449.928195, '$report_type': 'TestReport', 'item_index': 431, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_loop.py::test_loop_two_variables_single_backpropagation + location: ('tests/test_loop.py', 148, 'test_loop_two_variables_single_backpropagation') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_secondary_files_output + location: ('tests/test_provenance.py', 160, 'test_secondary_files_output') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_output', 'location': ('tests/test_provenance.py', 160, 'test_secondary_files_output'), 'keywords': {'test_secondary_files_output': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0010687859994504834, 'start': 1685951449.9292428, 'stop': 1685951449.930312, '$report_type': 'TestReport', 'item_index': 530, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters7-result7]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters7-result7]'), 'keywords': {'test_overrides[parameters7-result7]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters7-result7': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\'\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.cwl] /private/tmp/docker_tmp_n9dj204$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmp_n9dj204/cwl.output.json\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool_v1.1.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool_v1.1.cwl] {\n "in": "hello test env",\n "https://w3id.org/cwl/cwl#requirements": [\n {\n "class": "EnvVarRequirement",\n "envDef": [\n {\n "envName": "TEST_ENV",\n "envValue": "$(inputs.in)"\n }\n ]\n }\n ]\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool_v1.1.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool_v1.1.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo {\\\\\\"value\\\\\\": \\\\\\"$TEST_ENV\\\\\\"}"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool_v1.1.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool_v1.1.cwl] /private/tmp/docker_tmp_n9dj204$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmp_n9dj204/cwl.output.json\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:1222 Raw output from /private/tmp/docker_tmp_n9dj204/cwl.output.json: {\n "value": "hello test env"\n}\nINFO cwltool:job.py:419 [job env-tool_v1.1.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool_v1.1.cwl] outputs {\n "value": "hello test env"\n}\nDEBUG cwltool:job.py:446 [job env-tool_v1.1.cwl] Removing input staging directory /private/tmp/docker_tmpgx1egott\nDEBUG cwltool:job.py:454 [job env-tool_v1.1.cwl] Removing temporary directory /private/tmp/docker_tmpp_di2gaz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_n9dj204\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.8655887819995769, 'start': 1685951449.143234, 'stop': 1685951450.008804, '$report_type': 'TestReport', 'item_index': 474, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters7-result7]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters7-result7]'), 'keywords': {'test_overrides[parameters7-result7]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters7-result7': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\'\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.cwl] /private/tmp/docker_tmp_n9dj204$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmp_n9dj204/cwl.output.json\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool_v1.1.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool_v1.1.cwl] {\n "in": "hello test env",\n "https://w3id.org/cwl/cwl#requirements": [\n {\n "class": "EnvVarRequirement",\n "envDef": [\n {\n "envName": "TEST_ENV",\n "envValue": "$(inputs.in)"\n }\n ]\n }\n ]\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool_v1.1.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool_v1.1.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo {\\\\\\"value\\\\\\": \\\\\\"$TEST_ENV\\\\\\"}"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool_v1.1.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool_v1.1.cwl] /private/tmp/docker_tmp_n9dj204$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmp_n9dj204/cwl.output.json\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:1222 Raw output from /private/tmp/docker_tmp_n9dj204/cwl.output.json: {\n "value": "hello test env"\n}\nINFO cwltool:job.py:419 [job env-tool_v1.1.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool_v1.1.cwl] outputs {\n "value": "hello test env"\n}\nDEBUG cwltool:job.py:446 [job env-tool_v1.1.cwl] Removing input staging directory /private/tmp/docker_tmpgx1egott\nDEBUG cwltool:job.py:454 [job env-tool_v1.1.cwl] Removing temporary directory /private/tmp/docker_tmpp_di2gaz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_n9dj204\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008864490000632941, 'start': 1685951450.01002, 'stop': 1685951450.0109088, '$report_type': 'TestReport', 'item_index': 474, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides[parameters7-result7] + location: ('tests/test_override.py', 76, 'test_overrides[parameters7-result7]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides[parameters8-result8] + location: ('tests/test_override.py', 76, 'test_overrides[parameters8-result8]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters8-result8]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters8-result8]'), 'keywords': {'test_overrides[parameters8-result8]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters8-result8': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007296699996004463, 'start': 1685951450.0127401, 'stop': 1685951450.013471, '$report_type': 'TestReport', 'item_index': 475, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]'), 'keywords': {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task1_13\nDEBUG cwltool:workflow_job.py:727 [step task1_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_13\nDEBUG cwltool:command_line_tool.py:988 [job task1_11] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_11), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task2_13\nDEBUG cwltool:workflow_job.py:727 [step task2_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_13\nDEBUG cwltool:command_line_tool.py:988 [job task2_11] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_11] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_11), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_11] initial work dir {}\nINFO cwltool:job.py:266 [job task1_11] /private/tmp/docker_tmp4m9l14lt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp4m9l14lt,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpexenol_6,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-096004.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:266 [job task2_11] /private/tmp/docker_tmpq2su4gxh$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpq2su4gxh,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmplu6a4tzl,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-110322.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task1_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_11] completed success\nDEBUG cwltool:job.py:422 [job task1_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp4m9l14lt/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_13] completed success\nDEBUG cwltool:job.py:446 [job task1_11] Removing input staging directory /private/tmp/docker_tmpqp3usw7p\nDEBUG cwltool:job.py:454 [job task1_11] Removing temporary directory /private/tmp/docker_tmpexenol_6\nINFO cwltool:job.py:905 [job task2_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_11] completed success\nDEBUG cwltool:job.py:422 [job task2_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpq2su4gxh/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_13] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {}\nDEBUG cwltool:job.py:446 [job task2_11] Removing input staging directory /private/tmp/docker_tmp7r_dkuxt\nDEBUG cwltool:job.py:454 [job task2_11] Removing temporary directory /private/tmp/docker_tmplu6a4tzl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp4m9l14lt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzpg9e3kx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpq2su4gxh\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.7110078599998815, 'start': 1685951447.425432, 'stop': 1685951450.136374, '$report_type': 'TestReport', 'item_index': 279, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]'), 'keywords': {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task1_13\nDEBUG cwltool:workflow_job.py:727 [step task1_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_13\nDEBUG cwltool:command_line_tool.py:988 [job task1_11] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_11), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task2_13\nDEBUG cwltool:workflow_job.py:727 [step task2_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_13\nDEBUG cwltool:command_line_tool.py:988 [job task2_11] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_11] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_11), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_11] initial work dir {}\nINFO cwltool:job.py:266 [job task1_11] /private/tmp/docker_tmp4m9l14lt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp4m9l14lt,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpexenol_6,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-096004.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:266 [job task2_11] /private/tmp/docker_tmpq2su4gxh$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpq2su4gxh,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmplu6a4tzl,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-110322.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task1_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_11] completed success\nDEBUG cwltool:job.py:422 [job task1_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp4m9l14lt/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_13] completed success\nDEBUG cwltool:job.py:446 [job task1_11] Removing input staging directory /private/tmp/docker_tmpqp3usw7p\nDEBUG cwltool:job.py:454 [job task1_11] Removing temporary directory /private/tmp/docker_tmpexenol_6\nINFO cwltool:job.py:905 [job task2_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_11] completed success\nDEBUG cwltool:job.py:422 [job task2_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpq2su4gxh/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_13] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {}\nDEBUG cwltool:job.py:446 [job task2_11] Removing input staging directory /private/tmp/docker_tmp7r_dkuxt\nDEBUG cwltool:job.py:454 [job task2_11] Removing temporary directory /private/tmp/docker_tmplu6a4tzl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp4m9l14lt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzpg9e3kx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpq2su4gxh\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006579000000783708, 'start': 1685951450.137392, 'stop': 1685951450.138051, '$report_type': 'TestReport', 'item_index': 279, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] + location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\uadf8\\ub798\\ud504]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]'), 'keywords': {'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0021395619996837922, 'start': 1685951450.139597, 'stop': 1685951450.141738, '$report_type': 'TestReport', 'item_index': 505, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_require_prefix_networkaccess', 'location': ('tests/test_ext.py', 234, 'test_require_prefix_networkaccess'), 'keywords': {'test_require_prefix_networkaccess': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', '[worker-gw2] received command runtests {\'indices\': [497, 498, 499, 500, 501, 502, 503, 504]}\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] /private/tmp/docker_tmp75dfw90k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp75dfw90k,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp2jf3vw_z,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp1vsmbt9j/20230605095047-484284.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import urllib.request\nassert(urllib.request.urlopen("http://commonwl.org").code == 200)\n\'\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/networkaccess.cwl:6:1: checking field \'requirements\'\ntests/wf/networkaccess.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#NetworkAccess\'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/networkaccess-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/networkaccess-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/NetworkAccess\'\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job networkaccess.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\nDEBUG cwltool:command_line_tool.py:988 [job networkaccess.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job networkaccess.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job networkaccess.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "valueFrom": "import urllib.request\\nassert(urllib.request.urlopen(\\"http://commonwl.org\\").code == 200)\\n",\n "position": [\n 0,\n 1\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job networkaccess.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job networkaccess.cwl] /private/tmp/docker_tmp75dfw90k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp75dfw90k,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp2jf3vw_z,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp1vsmbt9j/20230605095047-484284.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import urllib.request\nassert(urllib.request.urlopen("http://commonwl.org").code == 200)\n\'\nINFO cwltool:job.py:905 [job networkaccess.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job networkaccess.cwl] completed success\nDEBUG cwltool:job.py:422 [job networkaccess.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job networkaccess.cwl] Removing input staging directory /private/tmp/docker_tmp9kgn1gg0\nDEBUG cwltool:job.py:454 [job networkaccess.cwl] Removing temporary directory /private/tmp/docker_tmp2jf3vw_z\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp75dfw90k\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/networkaccess.cwl:6:1: checking field \'requirements\'\ntests/wf/networkaccess.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#NetworkAccess\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/networkaccess-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/networkaccess-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/NetworkAccess\'')], 'duration': 3.5653393000002325, 'start': 1685951446.647063, 'stop': 1685951450.2123148, '$report_type': 'TestReport', 'item_index': 376, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_require_prefix_networkaccess', 'location': ('tests/test_ext.py', 234, 'test_require_prefix_networkaccess'), 'keywords': {'test_require_prefix_networkaccess': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', '[worker-gw2] received command runtests {\'indices\': [497, 498, 499, 500, 501, 502, 503, 504]}\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] /private/tmp/docker_tmp75dfw90k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp75dfw90k,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp2jf3vw_z,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp1vsmbt9j/20230605095047-484284.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import urllib.request\nassert(urllib.request.urlopen("http://commonwl.org").code == 200)\n\'\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/networkaccess.cwl:6:1: checking field \'requirements\'\ntests/wf/networkaccess.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#NetworkAccess\'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/networkaccess-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/networkaccess-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/NetworkAccess\'\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job networkaccess.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\nDEBUG cwltool:command_line_tool.py:988 [job networkaccess.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job networkaccess.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job networkaccess.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "valueFrom": "import urllib.request\\nassert(urllib.request.urlopen(\\"http://commonwl.org\\").code == 200)\\n",\n "position": [\n 0,\n 1\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job networkaccess.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job networkaccess.cwl] /private/tmp/docker_tmp75dfw90k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp75dfw90k,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp2jf3vw_z,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp1vsmbt9j/20230605095047-484284.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import urllib.request\nassert(urllib.request.urlopen("http://commonwl.org").code == 200)\n\'\nINFO cwltool:job.py:905 [job networkaccess.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job networkaccess.cwl] completed success\nDEBUG cwltool:job.py:422 [job networkaccess.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job networkaccess.cwl] Removing input staging directory /private/tmp/docker_tmp9kgn1gg0\nDEBUG cwltool:job.py:454 [job networkaccess.cwl] Removing temporary directory /private/tmp/docker_tmp2jf3vw_z\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp75dfw90k\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/networkaccess.cwl:6:1: checking field \'requirements\'\ntests/wf/networkaccess.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#NetworkAccess\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/networkaccess-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/networkaccess-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/NetworkAccess\'')], 'duration': 0.0005908630000703852, 'start': 1685951450.2137191, 'stop': 1685951450.2143118, '$report_type': 'TestReport', 'item_index': 376, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_require_prefix_networkaccess + location: ('tests/test_ext.py', 234, 'test_require_prefix_networkaccess') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_ext.py::test_require_prefix_workreuse + location: ('tests/test_ext.py', 241, 'test_require_prefix_workreuse') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_require_prefix_workreuse', 'location': ('tests/test_ext.py', 241, 'test_require_prefix_workreuse'), 'keywords': {'test_require_prefix_workreuse': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001844295999944734, 'start': 1685951450.21582, 'stop': 1685951450.2176661, '$report_type': 'TestReport', 'item_index': 377, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters8-result8]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters8-result8]'), 'keywords': {'test_overrides[parameters8-result8]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters8-result8': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\'\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.0-dev1.cwl] /private/tmp/docker_tmpx8gydkjw$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmpx8gydkjw/cwl.output.json\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.0-dev1.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml",\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env-tool_v1.1.0-dev1.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool_v1.1.0-dev1.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool_v1.1.0-dev1.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool_v1.1.0-dev1.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo {\\\\\\"value\\\\\\": \\\\\\"$TEST_ENV\\\\\\"}"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool_v1.1.0-dev1.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool_v1.1.0-dev1.cwl] /private/tmp/docker_tmpx8gydkjw$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmpx8gydkjw/cwl.output.json\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:1222 Raw output from /private/tmp/docker_tmpx8gydkjw/cwl.output.json: {\n "value": "hello test env"\n}\nINFO cwltool:job.py:419 [job env-tool_v1.1.0-dev1.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool_v1.1.0-dev1.cwl] outputs {\n "value": "hello test env"\n}\nDEBUG cwltool:job.py:446 [job env-tool_v1.1.0-dev1.cwl] Removing input staging directory /private/tmp/docker_tmpy3kullbt\nDEBUG cwltool:job.py:454 [job env-tool_v1.1.0-dev1.cwl] Removing temporary directory /private/tmp/docker_tmpkbnw1n9q\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpx8gydkjw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7702155999995739, 'start': 1685951450.0139031, 'stop': 1685951450.7841, '$report_type': 'TestReport', 'item_index': 475, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides[parameters8-result8]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters8-result8]'), 'keywords': {'test_overrides[parameters8-result8]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters8-result8': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\'\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.0-dev1.cwl] /private/tmp/docker_tmpx8gydkjw$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmpx8gydkjw/cwl.output.json\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.0-dev1.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml",\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env-tool_v1.1.0-dev1.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool_v1.1.0-dev1.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool_v1.1.0-dev1.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool_v1.1.0-dev1.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo {\\\\\\"value\\\\\\": \\\\\\"$TEST_ENV\\\\\\"}"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool_v1.1.0-dev1.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool_v1.1.0-dev1.cwl] /private/tmp/docker_tmpx8gydkjw$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmpx8gydkjw/cwl.output.json\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:1222 Raw output from /private/tmp/docker_tmpx8gydkjw/cwl.output.json: {\n "value": "hello test env"\n}\nINFO cwltool:job.py:419 [job env-tool_v1.1.0-dev1.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool_v1.1.0-dev1.cwl] outputs {\n "value": "hello test env"\n}\nDEBUG cwltool:job.py:446 [job env-tool_v1.1.0-dev1.cwl] Removing input staging directory /private/tmp/docker_tmpy3kullbt\nDEBUG cwltool:job.py:454 [job env-tool_v1.1.0-dev1.cwl] Removing temporary directory /private/tmp/docker_tmpkbnw1n9q\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpx8gydkjw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005138289998285472, 'start': 1685951450.785271, 'stop': 1685951450.7857862, '$report_type': 'TestReport', 'item_index': 475, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides[parameters8-result8] + location: ('tests/test_override.py', 76, 'test_overrides[parameters8-result8]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1] + location: ('tests/test_override.py', 119, 'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]'), 'keywords': {'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005757640001320397, 'start': 1685951450.787252, 'stop': 1685951450.787829, '$report_type': 'TestReport', 'item_index': 476, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\uadf8\\ub798\\ud504]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]'), 'keywords': {'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "그래프",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmplyn4vznq\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\nDEBUG cwltool:command_line_tool.py:988 [job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script] initial work dir {}\nINFO cwltool:job.py:266 [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script] completed success\nDEBUG cwltool:job.py:422 [job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\nDEBUG cwltool:job.py:454 [job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplyn4vznq\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7623934020002707, 'start': 1685951450.142199, 'stop': 1685951450.9045749, '$report_type': 'TestReport', 'item_index': 505, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\uadf8\\ub798\\ud504]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]'), 'keywords': {'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": 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/private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script] completed success\nDEBUG cwltool:job.py:422 [job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\nDEBUG cwltool:job.py:454 [job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplyn4vznq\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008543869998902665, 'start': 1685951450.9057658, 'stop': 1685951450.906623, '$report_type': 'TestReport', 'item_index': 505, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]'), 'keywords': {'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0022306440005195327, 'start': 1685951450.908751, 'stop': 1685951450.910984, '$report_type': 'TestReport', 'item_index': 506, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_output', 'location': ('tests/test_provenance.py', 160, 'test_secondary_files_output'), 'keywords': {'test_secondary_files_output': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "file1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt",\n "basename": "f.txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size",\n "class": "File",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter",\n "class": "File",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwjr18vof/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmptl8e6f9x$ /bin/sh \\\n -c \\\n echo "abc" > f.txt; echo "3" > f.txt.size; echo "a" > f.txt.firstletter; echo "a,b,c" > f.csv; echo "1,2,3" > f.csv.columns; echo "ignored" > f.txt.ignoreme;\n\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: dbf5eef1a93906a11f500e9f6a94d8f65d608284 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: ef33879db2f10ebed5a6b3bc3a12dea6059dfd003dfff5a196e5f85eaadf2ba0 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 833b03ecbda05d8947f87e51d289011e1d071e5e9a02a7d74e2f7e1d8e99a937f05b32f4a4112179a0bd8d635922da1de2ce6915597922a9e1580d2207dc386f workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwjr18vof/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/9ce15f63-7b5f-4e14-9592-43f785c1656c as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "echo \\"abc\\" > f.txt; echo \\"3\\" > f.txt.size; echo \\"a\\" > f.txt.firstletter; echo \\"a,b,c\\" > f.csv; echo \\"1,2,3\\" > f.csv.columns; echo \\"ignored\\" > f.txt.ignoreme;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmptl8e6f9x$ /bin/sh \\\n -c \\\n echo "abc" > f.txt; echo "3" > f.txt.size; echo "a" > f.txt.firstletter; echo "a,b,c" > f.csv; echo "1,2,3" > f.csv.columns; echo "ignored" > f.txt.ignoreme;\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 03cfd743661f07975fa2f1220c5194cbaff48451 data/03/03cfd743661f07975fa2f1220c5194cbaff48451\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: a3db5c13ff90a36963278c6a39e4ee3c22e2a436 data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 3f786850e387550fdab836ed7e6dc881de23001b data/3f/3f786850e387550fdab836ed7e6dc881de23001b\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 0f8ae3519acea73e158af005549dc58e8eb5d0df data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 593706831ae6760bd8b9a98b9204880a72f808c6 data/59/593706831ae6760bd8b9a98b9204880a72f808c6\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/59/593706831ae6760bd8b9a98b9204880a72f808c6\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/59/593706831ae6760bd8b9a98b9204880a72f808c6\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n },\n "file1csv": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "basename": "f.csv",\n "nameroot": "f",\n "nameext": ".csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "secondaryFiles": [\n {\n "basename": "f.csv.columns",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv.columns",\n "class": "File",\n "nameroot": "f.csv",\n "nameext": ".columns",\n "checksum": "sha1$593706831ae6760bd8b9a98b9204880a72f808c6",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:cbcd92ce-fff6-4c77-a6c7-d6e90f6ecef0"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:ea8d845d-f973-4952-b50d-2915b1ddb73d"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/file1csv": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "basename": "f.csv",\n "nameroot": "f",\n "nameext": ".csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "secondaryFiles": [\n {\n "basename": "f.csv.columns",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv.columns",\n "class": "File",\n "nameroot": "f.csv",\n "nameext": ".columns",\n "checksum": "sha1$593706831ae6760bd8b9a98b9204880a72f808c6",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:cbcd92ce-fff6-4c77-a6c7-d6e90f6ecef0"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:ea8d845d-f973-4952-b50d-2915b1ddb73d"\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n }\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpu3a4n93r\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpx5c78te_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt.size to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt.firstletter to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.csv to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp189hqv35\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptl8e6f9x\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: fa92c9177177f936cdd0212b7b26446ea28cda99 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: e8de14296bbe27af77d4f898752453ca0034c6e198bc62d313d5a579e1663daf metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: d01a3442648b65bf2246d43c7d33a60bf8b48c4ea713be0baaa70d16b6b7d8e008040c6329389c9dd5f095167440bfeb6af99df72e95e0ad4907eb6316c07210 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 71a7df0e199fb2b9fd211d58ffd07a30fb7c63e2 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 74355e4ddd99d82d89f79a29c332af5e3ca949b5e8d7e26ea0b2ceec527a3a94 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: e3750188dcebc789f166c32c097e9fa2a2fe93ab80a2c81dcae3a2bb87031d6a436e73e8362cd31cf4643d0454a813b27bf784b36b0082dca16920046439b7e1 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 176d0de5b0e0a92d27b39c355a386e3dc8497d18 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: de346266db74f4c6868e657e65e0491bb1053623ef10893e2ef289ae72bb79bf metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 5e470078ea0bc32960168987f8879cd4aea325c19979cd6f62d531892033051c64dff7cf33a72563a8ea7afd6cb51f833ca8da8fb4aa0ad540aff8955739b8ed metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 7982b196c67c4c3a50cc5da7613a0adc7c5424c5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: efda73edb11c091d10d96ba2d0a6bdfc46f110e30ea732beecb21ae2f3be6e94 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 7b86ec13244c7a658df1e8bc3f86ae8c6fa6d8b02fca043d61fb390190dc126110f7f5eb644dbe9dc48f3808b6e3fb52a6aab75dc797d7f34e72ad0ab5f45d8c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: bf4bd610c999085234872c8249d99c9de12b411c metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: fae8f3f405ca5c887e358d3814e056171235190eadc776a5317704828023746a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 37102c6ced82c58acc6241193c569132fd3e2dcfab1e201746c0bbd401a65a65c77d81de9d3f5745cf8c74dc153ab872097ad0983c4f6e77ca5370241c017b3a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 3687158ff1b66b5561e0b43be70b77107f40ee0d metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 8405cb03c17012e3e3733e54ea1feac3ecd232d0e767ed6536ac32a65fedb970 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: ef891c640d1e6f76eb404fb08cea726d4ad1ed73f482796d8162fd8b5e10531dce2708a95d0f63b4b3cda1893ce92a5a6c4bdbf1200952e8db9662c8318ef0b5 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\', \'basename\': \'f.txt\', \'nameroot\': \'f\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$03cfd743661f07975fa2f1220c5194cbaff48451\', \'size\': 4, \'secondaryFiles\': [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}], \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\', \'basename\': \'f.txt\', \'nameroot\': \'f\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$03cfd743661f07975fa2f1220c5194cbaff48451\', \'size\': 4, \'secondaryFiles\': [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}], \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt.size\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .size\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt.firstletter\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .firstletter\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.csv\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .csv\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 6\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 3ffb077462a7366ed56387657cf594c9b0d1b2c7 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 1444a80bd29d7069612ee7da6e0827aa7753a7bbbe2aa2630dc7f5432a4afdf9 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 5dbcb8f2cae6ccaa2629dfaa958aa306d53f9c8b9dd9f4b6c0d0606cbc049234c5b980005888ea539e94878a4309913e66370e8acebd1be4f35431fd8a3b5a9d workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: c5748d1251c37c7867c3c1d862c07b9878312eaa snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 67a63dbce041f71b377337196622308a9878245770761c1f262f81c4f4947def snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: d6a23fcdcb8ad33277e282d1bbd6fa38b8e50acb9daed31c45d92cbd61eacdb6445a0f2a22b01d78cf461962606db623e3dbcf9dbfa25cd44257b29b34a6a995 snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 537134b46bec1dfd4f639062130613c13a21bb65 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: a7d8e1cddfa8aaf793a2bba0d6293c722c561ec47575d81ffeb98914f0683848 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 8072951e1ca5d3fea48562d150dfce861b21dd5cce224f15b3ee21810e7fef677b41b9cff70bbbcf7cc9ad3246e4664295778a9c25ebbb1294febfc3c72894e3 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 0498f7f4009a5a84331e8b24fb83650d30af83f0 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 7b7f4ea36d4cdac950c799f82d0fa998385ce568888d640d77383d932914cbfe metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 3354b68c419ef9993f09b8f084a51a301bc44796df1f8535af054070a5b3d2b8e4d4e6579e58eb000c302a8ae10337ab989120f97f6734f3a11c0c5005b9b4ae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 688538bd7ce28063bf00184b1b965ba4aafece24 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 1c399bf2f5bd0fe13f29342156ec3a743516ab188f2b4c711fb37651ae68a222 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 25c66d4ed947eca4529f5722e7df143e89d14da48cbe3c502f98efd1c89571335c0e9392606635a402b04ac46b369a40c05a6c089278dec1872b42a821a2c213 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance')], 'duration': 1.1671647269995447, 'start': 1685951449.93065, 'stop': 1685951451.097787, '$report_type': 'TestReport', 'item_index': 530, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_output', 'location': ('tests/test_provenance.py', 160, 'test_secondary_files_output'), 'keywords': {'test_secondary_files_output': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "file1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt",\n "basename": "f.txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size",\n "class": "File",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter",\n "class": "File",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwjr18vof/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmptl8e6f9x$ /bin/sh \\\n -c \\\n echo "abc" > f.txt; echo "3" > f.txt.size; echo "a" > f.txt.firstletter; echo "a,b,c" > f.csv; echo "1,2,3" > f.csv.columns; echo "ignored" > f.txt.ignoreme;\n\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: dbf5eef1a93906a11f500e9f6a94d8f65d608284 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: ef33879db2f10ebed5a6b3bc3a12dea6059dfd003dfff5a196e5f85eaadf2ba0 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 833b03ecbda05d8947f87e51d289011e1d071e5e9a02a7d74e2f7e1d8e99a937f05b32f4a4112179a0bd8d635922da1de2ce6915597922a9e1580d2207dc386f workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwjr18vof/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/9ce15f63-7b5f-4e14-9592-43f785c1656c as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "echo \\"abc\\" > f.txt; echo \\"3\\" > f.txt.size; echo \\"a\\" > f.txt.firstletter; echo \\"a,b,c\\" > f.csv; echo \\"1,2,3\\" > f.csv.columns; echo \\"ignored\\" > f.txt.ignoreme;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmptl8e6f9x$ /bin/sh \\\n -c \\\n echo "abc" > f.txt; echo "3" > f.txt.size; echo "a" > f.txt.firstletter; echo "a,b,c" > f.csv; echo "1,2,3" > f.csv.columns; echo "ignored" > f.txt.ignoreme;\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 03cfd743661f07975fa2f1220c5194cbaff48451 data/03/03cfd743661f07975fa2f1220c5194cbaff48451\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: a3db5c13ff90a36963278c6a39e4ee3c22e2a436 data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 3f786850e387550fdab836ed7e6dc881de23001b data/3f/3f786850e387550fdab836ed7e6dc881de23001b\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 0f8ae3519acea73e158af005549dc58e8eb5d0df data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 593706831ae6760bd8b9a98b9204880a72f808c6 data/59/593706831ae6760bd8b9a98b9204880a72f808c6\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/59/593706831ae6760bd8b9a98b9204880a72f808c6\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/59/593706831ae6760bd8b9a98b9204880a72f808c6\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n },\n "file1csv": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "basename": "f.csv",\n "nameroot": "f",\n "nameext": ".csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "secondaryFiles": [\n {\n "basename": "f.csv.columns",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv.columns",\n "class": "File",\n "nameroot": "f.csv",\n "nameext": ".columns",\n "checksum": "sha1$593706831ae6760bd8b9a98b9204880a72f808c6",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:cbcd92ce-fff6-4c77-a6c7-d6e90f6ecef0"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:ea8d845d-f973-4952-b50d-2915b1ddb73d"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/file1csv": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "basename": "f.csv",\n "nameroot": "f",\n "nameext": ".csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "secondaryFiles": [\n {\n "basename": "f.csv.columns",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv.columns",\n "class": "File",\n "nameroot": "f.csv",\n "nameext": ".columns",\n "checksum": "sha1$593706831ae6760bd8b9a98b9204880a72f808c6",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:cbcd92ce-fff6-4c77-a6c7-d6e90f6ecef0"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:ea8d845d-f973-4952-b50d-2915b1ddb73d"\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n }\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpu3a4n93r\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpx5c78te_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt.size to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt.firstletter to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.csv to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp189hqv35\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptl8e6f9x\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: fa92c9177177f936cdd0212b7b26446ea28cda99 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: e8de14296bbe27af77d4f898752453ca0034c6e198bc62d313d5a579e1663daf metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: d01a3442648b65bf2246d43c7d33a60bf8b48c4ea713be0baaa70d16b6b7d8e008040c6329389c9dd5f095167440bfeb6af99df72e95e0ad4907eb6316c07210 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 71a7df0e199fb2b9fd211d58ffd07a30fb7c63e2 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 74355e4ddd99d82d89f79a29c332af5e3ca949b5e8d7e26ea0b2ceec527a3a94 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: e3750188dcebc789f166c32c097e9fa2a2fe93ab80a2c81dcae3a2bb87031d6a436e73e8362cd31cf4643d0454a813b27bf784b36b0082dca16920046439b7e1 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 176d0de5b0e0a92d27b39c355a386e3dc8497d18 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: de346266db74f4c6868e657e65e0491bb1053623ef10893e2ef289ae72bb79bf metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 5e470078ea0bc32960168987f8879cd4aea325c19979cd6f62d531892033051c64dff7cf33a72563a8ea7afd6cb51f833ca8da8fb4aa0ad540aff8955739b8ed metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 7982b196c67c4c3a50cc5da7613a0adc7c5424c5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: efda73edb11c091d10d96ba2d0a6bdfc46f110e30ea732beecb21ae2f3be6e94 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 7b86ec13244c7a658df1e8bc3f86ae8c6fa6d8b02fca043d61fb390190dc126110f7f5eb644dbe9dc48f3808b6e3fb52a6aab75dc797d7f34e72ad0ab5f45d8c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: bf4bd610c999085234872c8249d99c9de12b411c metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: fae8f3f405ca5c887e358d3814e056171235190eadc776a5317704828023746a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 37102c6ced82c58acc6241193c569132fd3e2dcfab1e201746c0bbd401a65a65c77d81de9d3f5745cf8c74dc153ab872097ad0983c4f6e77ca5370241c017b3a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 3687158ff1b66b5561e0b43be70b77107f40ee0d metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 8405cb03c17012e3e3733e54ea1feac3ecd232d0e767ed6536ac32a65fedb970 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: ef891c640d1e6f76eb404fb08cea726d4ad1ed73f482796d8162fd8b5e10531dce2708a95d0f63b4b3cda1893ce92a5a6c4bdbf1200952e8db9662c8318ef0b5 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\', \'basename\': \'f.txt\', \'nameroot\': \'f\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$03cfd743661f07975fa2f1220c5194cbaff48451\', \'size\': 4, \'secondaryFiles\': [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}], \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\', \'basename\': \'f.txt\', \'nameroot\': \'f\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$03cfd743661f07975fa2f1220c5194cbaff48451\', \'size\': 4, \'secondaryFiles\': [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}], \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt.size\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .size\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt.firstletter\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .firstletter\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.csv\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .csv\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 6\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 3ffb077462a7366ed56387657cf594c9b0d1b2c7 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 1444a80bd29d7069612ee7da6e0827aa7753a7bbbe2aa2630dc7f5432a4afdf9 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 5dbcb8f2cae6ccaa2629dfaa958aa306d53f9c8b9dd9f4b6c0d0606cbc049234c5b980005888ea539e94878a4309913e66370e8acebd1be4f35431fd8a3b5a9d workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: c5748d1251c37c7867c3c1d862c07b9878312eaa snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 67a63dbce041f71b377337196622308a9878245770761c1f262f81c4f4947def snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: d6a23fcdcb8ad33277e282d1bbd6fa38b8e50acb9daed31c45d92cbd61eacdb6445a0f2a22b01d78cf461962606db623e3dbcf9dbfa25cd44257b29b34a6a995 snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 537134b46bec1dfd4f639062130613c13a21bb65 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: a7d8e1cddfa8aaf793a2bba0d6293c722c561ec47575d81ffeb98914f0683848 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 8072951e1ca5d3fea48562d150dfce861b21dd5cce224f15b3ee21810e7fef677b41b9cff70bbbcf7cc9ad3246e4664295778a9c25ebbb1294febfc3c72894e3 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 0498f7f4009a5a84331e8b24fb83650d30af83f0 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 7b7f4ea36d4cdac950c799f82d0fa998385ce568888d640d77383d932914cbfe metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 3354b68c419ef9993f09b8f084a51a301bc44796df1f8535af054070a5b3d2b8e4d4e6579e58eb000c302a8ae10337ab989120f97f6734f3a11c0c5005b9b4ae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 688538bd7ce28063bf00184b1b965ba4aafece24 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 1c399bf2f5bd0fe13f29342156ec3a743516ab188f2b4c711fb37651ae68a222 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 25c66d4ed947eca4529f5722e7df143e89d14da48cbe3c502f98efd1c89571335c0e9392606635a402b04ac46b369a40c05a6c089278dec1872b42a821a2c213 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance')], 'duration': 0.000757134000195947, 'start': 1685951451.099516, 'stop': 1685951451.100275, '$report_type': 'TestReport', 'item_index': 530, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_secondary_files_output + location: ('tests/test_provenance.py', 160, 'test_secondary_files_output') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + when: runtest + nodeid: tests/test_provenance.py::test_secondary_files_output + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_directory_workflow + location: ('tests/test_provenance.py', 169, 'test_directory_workflow') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow', 'location': ('tests/test_provenance.py', 169, 'test_directory_workflow'), 'keywords': {'test_directory_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001610086999789928, 'start': 1685951451.102933, 'stop': 1685951451.104544, '$report_type': 'TestReport', 'item_index': 531, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]'), 'keywords': {'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/formattest.cwl-tests/wf/formattest-job.json-True': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:49]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\n\x1b[1;30mINFO\x1b[0m [job formattest.cwl] /private/tmp/docker_tmp9uzslvog$ rev \\\n /private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt > /private/tmp/docker_tmp9uzslvog/output.txt\n\x1b[1;30mINFO\x1b[0m [job formattest.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck#main\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "dirname": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main] /private/tmp/docker_tmpr6g49v7h$ rev \\\n /private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt > /private/tmp/docker_tmpr6g49v7h/output.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpr6g49v7h/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] Removing input staging directory /private/tmp/docker_tmp3uoblnx6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] Removing temporary directory /private/tmp/docker_tmpekbfudg1\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpr6g49v7h/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpr6g49v7h\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job formattest.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\nDEBUG cwltool:command_line_tool.py:988 [job formattest.cwl] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job formattest.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job formattest.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt",\n "dirname": "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job formattest.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job formattest.cwl] /private/tmp/docker_tmp9uzslvog$ rev \\\n /private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt > /private/tmp/docker_tmp9uzslvog/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job formattest.cwl] completed success\nDEBUG cwltool:job.py:422 [job formattest.cwl] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp9uzslvog/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job formattest.cwl] Removing input staging directory /private/tmp/docker_tmpko9q_21s\nDEBUG cwltool:job.py:454 [job formattest.cwl] Removing temporary directory /private/tmp/docker_tmp5ylwymyc\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp9uzslvog/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9uzslvog\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\'\nDEBUG cwltool:command_line_tool.py:982 [job main] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck#main\nDEBUG cwltool:command_line_tool.py:988 [job main] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job main] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "dirname": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job main] initial work dir {}\nINFO cwltool:job.py:266 [job main] /private/tmp/docker_tmpr6g49v7h$ rev \\\n /private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt > /private/tmp/docker_tmpr6g49v7h/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main] completed success\nDEBUG cwltool:job.py:422 [job main] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpr6g49v7h/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job main] Removing input staging directory /private/tmp/docker_tmp3uoblnx6\nDEBUG cwltool:job.py:454 [job main] Removing temporary directory /private/tmp/docker_tmpekbfudg1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpr6g49v7h/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr6g49v7h\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.5225798010005747, 'start': 1685951449.591155, 'stop': 1685951451.113698, '$report_type': 'TestReport', 'item_index': 493, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]'), 'keywords': {'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/formattest.cwl-tests/wf/formattest-job.json-True': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:49]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\n\x1b[1;30mINFO\x1b[0m [job formattest.cwl] /private/tmp/docker_tmp9uzslvog$ rev \\\n /private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt > /private/tmp/docker_tmp9uzslvog/output.txt\n\x1b[1;30mINFO\x1b[0m [job formattest.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck#main\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "dirname": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main] /private/tmp/docker_tmpr6g49v7h$ rev \\\n /private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt > /private/tmp/docker_tmpr6g49v7h/output.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpr6g49v7h/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] Removing input staging directory /private/tmp/docker_tmp3uoblnx6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] Removing temporary directory /private/tmp/docker_tmpekbfudg1\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpr6g49v7h/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpr6g49v7h\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job formattest.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\nDEBUG cwltool:command_line_tool.py:988 [job formattest.cwl] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job formattest.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job formattest.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt",\n "dirname": "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job formattest.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job formattest.cwl] /private/tmp/docker_tmp9uzslvog$ rev \\\n /private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt > /private/tmp/docker_tmp9uzslvog/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job formattest.cwl] completed success\nDEBUG cwltool:job.py:422 [job formattest.cwl] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp9uzslvog/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job formattest.cwl] Removing input staging directory /private/tmp/docker_tmpko9q_21s\nDEBUG cwltool:job.py:454 [job formattest.cwl] Removing temporary directory /private/tmp/docker_tmp5ylwymyc\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp9uzslvog/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9uzslvog\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\'\nDEBUG cwltool:command_line_tool.py:982 [job main] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck#main\nDEBUG cwltool:command_line_tool.py:988 [job main] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job main] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "dirname": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job main] initial work dir {}\nINFO cwltool:job.py:266 [job main] /private/tmp/docker_tmpr6g49v7h$ rev \\\n /private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt > /private/tmp/docker_tmpr6g49v7h/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main] completed success\nDEBUG cwltool:job.py:422 [job main] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpr6g49v7h/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job main] Removing input staging directory /private/tmp/docker_tmp3uoblnx6\nDEBUG cwltool:job.py:454 [job main] Removing temporary directory /private/tmp/docker_tmpekbfudg1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpr6g49v7h/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr6g49v7h\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007574420005767024, 'start': 1685951451.114835, 'stop': 1685951451.115593, '$report_type': 'TestReport', 'item_index': 493, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True] + location: ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_parallel.py::test_sequential_workflow + location: ('tests/test_parallel.py', 10, 'test_sequential_workflow') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_parallel.py::test_sequential_workflow', 'location': ('tests/test_parallel.py', 10, 'test_sequential_workflow'), 'keywords': {'test_sequential_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013370579999900656, 'start': 1685951451.117016, 'stop': 1685951451.1183538, '$report_type': 'TestReport', 'item_index': 494, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]'), 'keywords': {'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool.cwl'\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\n`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1")], 'duration': 0.7309547619997829, 'start': 1685951450.788568, 'stop': 1685951451.519506, '$report_type': 'TestReport', 'item_index': 476, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]'), 'keywords': {'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool.cwl'\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\n`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1")], 'duration': 0.00033288000031461706, 'start': 1685951451.519996, 'stop': 1685951451.52033, '$report_type': 'TestReport', 'item_index': 476, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1] + location: ('tests/test_override.py', 119, 'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.] + location: ('tests/test_override.py', 119, "test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]") + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0010089769994010567, 'start': 1685951451.52194, 'stop': 1685951451.522951, '$report_type': 'TestReport', 'item_index': 477, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nVersion 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.")], 'duration': 0.026144765000026382, 'start': 1685951451.524121, 'stop': 1685951451.550267, '$report_type': 'TestReport', 'item_index': 477, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nVersion 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.")], 'duration': 0.000790431000496028, 'start': 1685951451.551027, 'stop': 1685951451.55182, '$report_type': 'TestReport', 'item_index': 477, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.] + location: ('tests/test_override.py', 119, "test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]") + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_override.py::test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.] + location: ('tests/test_override.py', 119, 'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]'), 'keywords': {'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006940140001461259, 'start': 1685951451.554448, 'stop': 1685951451.5551438, '$report_type': 'TestReport', 'item_index': 478, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]'), 'keywords': {'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml'\nERROR cwltool:main.py:1208 Tool definition failed validation:\n`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.")], 'duration': 0.027587419000155933, 'start': 1685951451.555978, 'stop': 1685951451.5835662, '$report_type': 'TestReport', 'item_index': 478, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]'), 'keywords': {'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml'\nERROR cwltool:main.py:1208 Tool definition failed validation:\n`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.")], 'duration': 0.0007339860003412468, 'start': 1685951451.5840719, 'stop': 1685951451.584807, '$report_type': 'TestReport', 'item_index': 478, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_override.py::test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.] + location: ('tests/test_override.py', 119, 'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_writable_bytes + location: ('tests/test_provenance.py', 664, 'test_writable_bytes') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_writable_bytes', 'location': ('tests/test_provenance.py', 664, 'test_writable_bytes'), 'keywords': {'test_writable_bytes': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u')], 'duration': 0.005912863000048674, 'start': 1685951451.5864651, 'stop': 1685951451.5923798, '$report_type': 'TestReport', 'item_index': 537, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_writable_bytes', 'location': ('tests/test_provenance.py', 664, 'test_writable_bytes'), 'keywords': {'test_writable_bytes': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha256.txt: bb16a101c183c6c35bd53683d04273e214e77926e039369f065b11df84b47c80 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha512.txt: e03ebad752a05a76268c9516807e8564af9a26827485e1e3525b06e1d784437a5e9455f764a9914f1a7b851ebfeab27127a5174955711b7e4fd2bfaa8057bd1b file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha256.txt: bb16a101c183c6c35bd53683d04273e214e77926e039369f065b11df84b47c80 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha512.txt: e03ebad752a05a76268c9516807e8564af9a26827485e1e3525b06e1d784437a5e9455f764a9914f1a7b851ebfeab27127a5174955711b7e4fd2bfaa8057bd1b file.txt')], 'duration': 0.004632062000382575, 'start': 1685951451.593941, 'stop': 1685951451.598576, '$report_type': 'TestReport', 'item_index': 537, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_writable_bytes', 'location': ('tests/test_provenance.py', 664, 'test_writable_bytes'), 'keywords': {'test_writable_bytes': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha256.txt: bb16a101c183c6c35bd53683d04273e214e77926e039369f065b11df84b47c80 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha512.txt: e03ebad752a05a76268c9516807e8564af9a26827485e1e3525b06e1d784437a5e9455f764a9914f1a7b851ebfeab27127a5174955711b7e4fd2bfaa8057bd1b file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha256.txt: bb16a101c183c6c35bd53683d04273e214e77926e039369f065b11df84b47c80 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha512.txt: e03ebad752a05a76268c9516807e8564af9a26827485e1e3525b06e1d784437a5e9455f764a9914f1a7b851ebfeab27127a5174955711b7e4fd2bfaa8057bd1b file.txt'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u')], 'duration': 0.0028034570004820125, 'start': 1685951451.5994, 'stop': 1685951451.602205, '$report_type': 'TestReport', 'item_index': 537, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_writable_bytes + location: ('tests/test_provenance.py', 664, 'test_writable_bytes') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_data + location: ('tests/test_provenance.py', 670, 'test_data') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_data', 'location': ('tests/test_provenance.py', 670, 'test_data'), 'keywords': {'test_data': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j')], 'duration': 0.007278058999872883, 'start': 1685951451.603891, 'stop': 1685951451.61117, '$report_type': 'TestReport', 'item_index': 538, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_data', 'location': ('tests/test_provenance.py', 670, 'test_data'), 'keywords': {'test_data': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/data/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha1.txt: 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 data/file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha256.txt: 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 data/file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha512.txt: c2bad2223811194582af4d1508ac02cd69eeeeedeeb98d54fcae4dcefb13cc882e7640328206603d3fb9cd5f949a9be0db054dd34fbfa190c498a5fe09750cef data/file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/data/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha1.txt: 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 data/file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha256.txt: 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 data/file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha512.txt: c2bad2223811194582af4d1508ac02cd69eeeeedeeb98d54fcae4dcefb13cc882e7640328206603d3fb9cd5f949a9be0db054dd34fbfa190c498a5fe09750cef data/file.txt')], 'duration': 0.0031968230005077203, 'start': 1685951451.611891, 'stop': 1685951451.615089, '$report_type': 'TestReport', 'item_index': 538, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_data', 'location': ('tests/test_provenance.py', 670, 'test_data'), 'keywords': {'test_data': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/data/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha1.txt: 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 data/file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha256.txt: 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 data/file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha512.txt: c2bad2223811194582af4d1508ac02cd69eeeeedeeb98d54fcae4dcefb13cc882e7640328206603d3fb9cd5f949a9be0db054dd34fbfa190c498a5fe09750cef data/file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/data/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha1.txt: 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 data/file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha256.txt: 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 data/file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha512.txt: c2bad2223811194582af4d1508ac02cd69eeeeedeeb98d54fcae4dcefb13cc882e7640328206603d3fb9cd5f949a9be0db054dd34fbfa190c498a5fe09750cef data/file.txt'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j')], 'duration': 0.002914530999987619, 'start': 1685951451.616121, 'stop': 1685951451.619037, '$report_type': 'TestReport', 'item_index': 538, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_data + location: ('tests/test_provenance.py', 670, 'test_data') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_not_seekable + location: ('tests/test_provenance.py', 684, 'test_not_seekable') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_procgenerator.py::test_missing_enable_ext', 'location': ('tests/test_procgenerator.py', 11, 'test_missing_enable_ext'), 'keywords': {'test_missing_enable_ext': 1, 'test_procgenerator.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw5] received command runtests {'indices': [525, 526, 527, 528, 529]}\n"), ('Captured stdout call', '{}{}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/generator/pytoolgen.cwl:5:1: Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#ProcessGenerator\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking object\n \'tests/wf/generator/pytoolgen.cwl#63b74b39-a071-4257-b29d-255fd3678eff\'\ntests/wf/generator/pytoolgen.cwl:20:3: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmprlvxti83/stg2af42b50-d1e6-4c94-88fd-f39581a3c50f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n true\n ],\n "_:3de4ddb3-d354-49a0-b40e-33b49f9cfcbc": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmpimru1mpg/inp.py",\n "CreateFile",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] /private/tmp/docker_tmpimru1mpg$ python \\\n inp.py > /private/tmp/docker_tmpimru1mpg/main.cwl\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmpimru1mpg/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing input staging directory /private/tmp/docker_tmprlvxti83\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing temporary directory /private/tmp/docker_tmpmsq9o_0c\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpimru1mpg/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpimru1mpg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] {\n "zing": "zipper"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main.cwl] /private/tmp/docker_tmpvu2jo5rk$ echo \\\n zipper\nzipper\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] outputs {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] Removing input staging directory /private/tmp/docker_tmp3wbe2izn\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] Removing temporary directory /private/tmp/docker_tmp3kxlbsg0\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvu2jo5rk\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mINFO\x1b[0m [job 07d993b3-177f-45a0-8789-6297c239ab04] /private/tmp/docker_tmp49cf7jpt$ python \\\n inp.py > /private/tmp/docker_tmp49cf7jpt/main.cwl\n\x1b[1;30mINFO\x1b[0m [job 07d993b3-177f-45a0-8789-6297c239ab04] completed success\n\x1b[1;30mINFO\x1b[0m [job main.cwl_2] /private/tmp/docker_tmpofjjqo7q$ echo \\\n zipper\nzipper\n\x1b[1;30mINFO\x1b[0m [job main.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/generator/pytoolgen.cwl:5:1: Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#ProcessGenerator\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking object\n \'tests/wf/generator/pytoolgen.cwl#63b74b39-a071-4257-b29d-255fd3678eff\'\ntests/wf/generator/pytoolgen.cwl:20:3: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e\nDEBUG cwltool:command_line_tool.py:988 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmprlvxti83/stg2af42b50-d1e6-4c94-88fd-f39581a3c50f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\nDEBUG cwltool:job.py:215 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n true\n ],\n "_:3de4ddb3-d354-49a0-b40e-33b49f9cfcbc": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmpimru1mpg/inp.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] /private/tmp/docker_tmpimru1mpg$ python \\\n inp.py > /private/tmp/docker_tmpimru1mpg/main.cwl\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] completed success\nDEBUG cwltool:job.py:422 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmpimru1mpg/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing input staging directory /private/tmp/docker_tmprlvxti83\nDEBUG cwltool:job.py:454 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing temporary directory /private/tmp/docker_tmpmsq9o_0c\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpimru1mpg/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpimru1mpg\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:982 [job main.cwl] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:command_line_tool.py:988 [job main.cwl] {\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job main.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\nDEBUG cwltool:job.py:215 [job main.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job main.cwl] /private/tmp/docker_tmpvu2jo5rk$ echo \\\n zipper\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main.cwl] completed success\nDEBUG cwltool:job.py:422 [job main.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job main.cwl] Removing input staging directory /private/tmp/docker_tmp3wbe2izn\nDEBUG cwltool:job.py:454 [job main.cwl] Removing temporary directory /private/tmp/docker_tmp3kxlbsg0\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvu2jo5rk\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job 07d993b3-177f-45a0-8789-6297c239ab04] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#07d993b3-177f-45a0-8789-6297c239ab04\nDEBUG cwltool:command_line_tool.py:988 [job 07d993b3-177f-45a0-8789-6297c239ab04] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job 07d993b3-177f-45a0-8789-6297c239ab04] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmpkqg74yut/stg22aa02e0-1fa4-463f-84cf-f80e2705270f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmp49cf7jpt/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmp49cf7jpt/pytoolgen.cwl",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job 07d993b3-177f-45a0-8789-6297c239ab04] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\nDEBUG cwltool:job.py:215 [job 07d993b3-177f-45a0-8789-6297c239ab04] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmp49cf7jpt/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmp49cf7jpt/pytoolgen.cwl",\n "File",\n true\n ],\n "_:899bc3cb-ab75-4248-84a3-8ca71a12aa7b": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmp49cf7jpt/inp.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 07d993b3-177f-45a0-8789-6297c239ab04] /private/tmp/docker_tmp49cf7jpt$ python \\\n inp.py > /private/tmp/docker_tmp49cf7jpt/main.cwl\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job 07d993b3-177f-45a0-8789-6297c239ab04] completed success\nDEBUG cwltool:job.py:422 [job 07d993b3-177f-45a0-8789-6297c239ab04] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmp49cf7jpt/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job 07d993b3-177f-45a0-8789-6297c239ab04] Removing input staging directory /private/tmp/docker_tmpkqg74yut\nDEBUG cwltool:job.py:454 [job 07d993b3-177f-45a0-8789-6297c239ab04] Removing temporary directory /private/tmp/docker_tmpfwqvipwz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp49cf7jpt/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp49cf7jpt\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:982 [job main.cwl_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:command_line_tool.py:988 [job main.cwl_2] {\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job main.cwl_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\nDEBUG cwltool:job.py:215 [job main.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job main.cwl_2] /private/tmp/docker_tmpofjjqo7q$ echo \\\n zipper\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job main.cwl_2] outputs {}\nDEBUG cwltool:job.py:446 [job main.cwl_2] Removing input staging directory /private/tmp/docker_tmp36cpw1ex\nDEBUG cwltool:job.py:454 [job main.cwl_2] Removing temporary directory /private/tmp/docker_tmp35m5sh1r\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpofjjqo7q\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.935050539000258, 'start': 1685951448.686326, 'stop': 1685951451.621305, '$report_type': 'TestReport', 'item_index': 522, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_procgenerator.py::test_missing_enable_ext', 'location': ('tests/test_procgenerator.py', 11, 'test_missing_enable_ext'), 'keywords': {'test_missing_enable_ext': 1, 'test_procgenerator.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw5] received command runtests {'indices': [525, 526, 527, 528, 529]}\n"), ('Captured stdout call', '{}{}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/generator/pytoolgen.cwl:5:1: Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#ProcessGenerator\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking object\n \'tests/wf/generator/pytoolgen.cwl#63b74b39-a071-4257-b29d-255fd3678eff\'\ntests/wf/generator/pytoolgen.cwl:20:3: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmprlvxti83/stg2af42b50-d1e6-4c94-88fd-f39581a3c50f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n true\n ],\n "_:3de4ddb3-d354-49a0-b40e-33b49f9cfcbc": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmpimru1mpg/inp.py",\n "CreateFile",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] /private/tmp/docker_tmpimru1mpg$ python \\\n inp.py > /private/tmp/docker_tmpimru1mpg/main.cwl\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmpimru1mpg/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing input staging directory /private/tmp/docker_tmprlvxti83\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing temporary directory /private/tmp/docker_tmpmsq9o_0c\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpimru1mpg/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpimru1mpg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] {\n "zing": "zipper"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main.cwl] /private/tmp/docker_tmpvu2jo5rk$ echo \\\n zipper\nzipper\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] outputs {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] Removing input staging directory /private/tmp/docker_tmp3wbe2izn\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] Removing temporary directory /private/tmp/docker_tmp3kxlbsg0\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvu2jo5rk\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mINFO\x1b[0m [job 07d993b3-177f-45a0-8789-6297c239ab04] /private/tmp/docker_tmp49cf7jpt$ python \\\n inp.py > /private/tmp/docker_tmp49cf7jpt/main.cwl\n\x1b[1;30mINFO\x1b[0m [job 07d993b3-177f-45a0-8789-6297c239ab04] completed success\n\x1b[1;30mINFO\x1b[0m [job main.cwl_2] /private/tmp/docker_tmpofjjqo7q$ echo \\\n zipper\nzipper\n\x1b[1;30mINFO\x1b[0m [job main.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/generator/pytoolgen.cwl:5:1: Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#ProcessGenerator\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking object\n \'tests/wf/generator/pytoolgen.cwl#63b74b39-a071-4257-b29d-255fd3678eff\'\ntests/wf/generator/pytoolgen.cwl:20:3: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e\nDEBUG cwltool:command_line_tool.py:988 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmprlvxti83/stg2af42b50-d1e6-4c94-88fd-f39581a3c50f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\nDEBUG cwltool:job.py:215 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n true\n ],\n "_:3de4ddb3-d354-49a0-b40e-33b49f9cfcbc": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmpimru1mpg/inp.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] /private/tmp/docker_tmpimru1mpg$ python \\\n inp.py > /private/tmp/docker_tmpimru1mpg/main.cwl\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] completed success\nDEBUG cwltool:job.py:422 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmpimru1mpg/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing input staging directory /private/tmp/docker_tmprlvxti83\nDEBUG cwltool:job.py:454 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing temporary directory /private/tmp/docker_tmpmsq9o_0c\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpimru1mpg/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpimru1mpg\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:982 [job main.cwl] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:command_line_tool.py:988 [job main.cwl] {\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job main.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\nDEBUG cwltool:job.py:215 [job main.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job main.cwl] /private/tmp/docker_tmpvu2jo5rk$ echo \\\n zipper\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main.cwl] completed success\nDEBUG cwltool:job.py:422 [job main.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job main.cwl] Removing input staging directory /private/tmp/docker_tmp3wbe2izn\nDEBUG cwltool:job.py:454 [job main.cwl] Removing temporary directory /private/tmp/docker_tmp3kxlbsg0\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvu2jo5rk\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job 07d993b3-177f-45a0-8789-6297c239ab04] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#07d993b3-177f-45a0-8789-6297c239ab04\nDEBUG cwltool:command_line_tool.py:988 [job 07d993b3-177f-45a0-8789-6297c239ab04] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job 07d993b3-177f-45a0-8789-6297c239ab04] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmpkqg74yut/stg22aa02e0-1fa4-463f-84cf-f80e2705270f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmp49cf7jpt/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmp49cf7jpt/pytoolgen.cwl",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job 07d993b3-177f-45a0-8789-6297c239ab04] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\nDEBUG cwltool:job.py:215 [job 07d993b3-177f-45a0-8789-6297c239ab04] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmp49cf7jpt/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmp49cf7jpt/pytoolgen.cwl",\n "File",\n true\n ],\n "_:899bc3cb-ab75-4248-84a3-8ca71a12aa7b": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmp49cf7jpt/inp.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 07d993b3-177f-45a0-8789-6297c239ab04] /private/tmp/docker_tmp49cf7jpt$ python \\\n inp.py > /private/tmp/docker_tmp49cf7jpt/main.cwl\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job 07d993b3-177f-45a0-8789-6297c239ab04] completed success\nDEBUG cwltool:job.py:422 [job 07d993b3-177f-45a0-8789-6297c239ab04] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmp49cf7jpt/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job 07d993b3-177f-45a0-8789-6297c239ab04] Removing input staging directory /private/tmp/docker_tmpkqg74yut\nDEBUG cwltool:job.py:454 [job 07d993b3-177f-45a0-8789-6297c239ab04] Removing temporary directory /private/tmp/docker_tmpfwqvipwz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp49cf7jpt/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp49cf7jpt\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:982 [job main.cwl_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:command_line_tool.py:988 [job main.cwl_2] {\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job main.cwl_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\nDEBUG cwltool:job.py:215 [job main.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job main.cwl_2] /private/tmp/docker_tmpofjjqo7q$ echo \\\n zipper\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job main.cwl_2] outputs {}\nDEBUG cwltool:job.py:446 [job main.cwl_2] Removing input staging directory /private/tmp/docker_tmp36cpw1ex\nDEBUG cwltool:job.py:454 [job main.cwl_2] Removing temporary directory /private/tmp/docker_tmp35m5sh1r\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpofjjqo7q\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0012447789995349012, 'start': 1685951451.6238, 'stop': 1685951451.625047, '$report_type': 'TestReport', 'item_index': 522, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_procgenerator.py::test_missing_enable_ext + location: ('tests/test_procgenerator.py', 11, 'test_missing_enable_ext') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_hello_workflow + location: ('tests/test_provenance.py', 49, 'test_hello_workflow') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_hello_workflow', 'location': ('tests/test_provenance.py', 49, 'test_hello_workflow'), 'keywords': {'test_hello_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014106010003160918, 'start': 1685951451.627031, 'stop': 1685951451.628444, '$report_type': 'TestReport', 'item_index': 523, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_not_seekable', 'location': ('tests/test_provenance.py', 684, 'test_not_seekable'), 'keywords': {'test_not_seekable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n')], 'duration': 0.008083244000772538, 'start': 1685951451.620725, 'stop': 1685951451.628809, '$report_type': 'TestReport', 'item_index': 539, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_not_seekable', 'location': ('tests/test_provenance.py', 684, 'test_not_seekable'), 'keywords': {'test_not_seekable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt')], 'duration': 0.0024598749996584957, 'start': 1685951451.629571, 'stop': 1685951451.632032, '$report_type': 'TestReport', 'item_index': 539, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_not_seekable', 'location': ('tests/test_provenance.py', 684, 'test_not_seekable'), 'keywords': {'test_not_seekable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n')], 'duration': 0.002072841999506636, 'start': 1685951451.632972, 'stop': 1685951451.635046, '$report_type': 'TestReport', 'item_index': 539, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_not_seekable + location: ('tests/test_provenance.py', 684, 'test_not_seekable') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_not_readable + location: ('tests/test_provenance.py', 691, 'test_not_readable') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_not_readable', 'location': ('tests/test_provenance.py', 691, 'test_not_readable'), 'keywords': {'test_not_readable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s')], 'duration': 0.005643378999593551, 'start': 1685951451.636606, 'stop': 1685951451.642252, '$report_type': 'TestReport', 'item_index': 540, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_not_readable', 'location': ('tests/test_provenance.py', 691, 'test_not_readable'), 'keywords': {'test_not_readable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt')], 'duration': 0.0024552830000175163, 'start': 1685951451.642875, 'stop': 1685951451.645331, '$report_type': 'TestReport', 'item_index': 540, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_not_readable', 'location': ('tests/test_provenance.py', 691, 'test_not_readable'), 'keywords': {'test_not_readable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s')], 'duration': 0.0030873249997966923, 'start': 1685951451.645994, 'stop': 1685951451.6490839, '$report_type': 'TestReport', 'item_index': 540, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_not_readable + location: ('tests/test_provenance.py', 691, 'test_not_readable') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_truncate_fails + location: ('tests/test_provenance.py', 698, 'test_truncate_fails') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_truncate_fails', 'location': ('tests/test_provenance.py', 698, 'test_truncate_fails'), 'keywords': {'test_truncate_fails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw3] received command runtests {'indices': [543, 544, 545, 546, 547]}\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33\x1b[0m\n"), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33')], 'duration': 0.006450511000366532, 'start': 1685951451.6508732, 'stop': 1685951451.6573272, '$report_type': 'TestReport', 'item_index': 541, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_truncate_fails', 'location': ('tests/test_provenance.py', 698, 'test_truncate_fails'), 'keywords': {'test_truncate_fails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw3] received command runtests {'indices': [543, 544, 545, 546, 547]}\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33\x1b[0m\n"), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha1.txt: 726c76553e1a3fdea29134f36e6af2ea05ec5cce file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha256.txt: 4e47826698bb4630fb4451010062fadbf85d61427cbdfaed7ad0f23f239bed89 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha512.txt: 567683ddba1f5a576b68ec26f41ffbcc7e718d646839ac6c2ef746fe952cef4cbe6dea635bc2f098b92b65caacf482333bb9d1d9a3089bc4f01cb86f7a2fbc18 file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha1.txt: 726c76553e1a3fdea29134f36e6af2ea05ec5cce file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha256.txt: 4e47826698bb4630fb4451010062fadbf85d61427cbdfaed7ad0f23f239bed89 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha512.txt: 567683ddba1f5a576b68ec26f41ffbcc7e718d646839ac6c2ef746fe952cef4cbe6dea635bc2f098b92b65caacf482333bb9d1d9a3089bc4f01cb86f7a2fbc18 file.txt')], 'duration': 0.0026148610004383954, 'start': 1685951451.658166, 'stop': 1685951451.6607842, '$report_type': 'TestReport', 'item_index': 541, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_truncate_fails', 'location': ('tests/test_provenance.py', 698, 'test_truncate_fails'), 'keywords': {'test_truncate_fails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw3] received command runtests {'indices': [543, 544, 545, 546, 547]}\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33\x1b[0m\n"), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha1.txt: 726c76553e1a3fdea29134f36e6af2ea05ec5cce file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha256.txt: 4e47826698bb4630fb4451010062fadbf85d61427cbdfaed7ad0f23f239bed89 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha512.txt: 567683ddba1f5a576b68ec26f41ffbcc7e718d646839ac6c2ef746fe952cef4cbe6dea635bc2f098b92b65caacf482333bb9d1d9a3089bc4f01cb86f7a2fbc18 file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha1.txt: 726c76553e1a3fdea29134f36e6af2ea05ec5cce file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha256.txt: 4e47826698bb4630fb4451010062fadbf85d61427cbdfaed7ad0f23f239bed89 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha512.txt: 567683ddba1f5a576b68ec26f41ffbcc7e718d646839ac6c2ef746fe952cef4cbe6dea635bc2f098b92b65caacf482333bb9d1d9a3089bc4f01cb86f7a2fbc18 file.txt'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33')], 'duration': 0.0020153519999439595, 'start': 1685951451.661279, 'stop': 1685951451.663295, '$report_type': 'TestReport', 'item_index': 541, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_truncate_fails + location: ('tests/test_provenance.py', 698, 'test_truncate_fails') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-0097-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-0097-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-0097-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-0097-True]'), 'keywords': {'test_check_mod_11_2[0000-0002-1825-0097-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-0097-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006354670003929641, 'start': 1685951451.66491, 'stop': 1685951451.665547, '$report_type': 'TestReport', 'item_index': 542, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-0097-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-0097-True]'), 'keywords': {'test_check_mod_11_2[0000-0002-1825-0097-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-0097-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00038638800015178276, 'start': 1685951451.666068, 'stop': 1685951451.666456, '$report_type': 'TestReport', 'item_index': 542, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-0097-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-0097-True]'), 'keywords': {'test_check_mod_11_2[0000-0002-1825-0097-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-0097-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00047956100024748594, 'start': 1685951451.667198, 'stop': 1685951451.667679, '$report_type': 'TestReport', 'item_index': 542, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-0097-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-0097-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0001-5109-3700-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0001-5109-3700-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0001-5109-3700-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0001-5109-3700-True]'), 'keywords': {'test_check_mod_11_2[0000-0001-5109-3700-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0001-5109-3700-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00046897900028852746, 'start': 1685951451.6689842, 'stop': 1685951451.669454, '$report_type': 'TestReport', 'item_index': 543, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0001-5109-3700-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0001-5109-3700-True]'), 'keywords': {'test_check_mod_11_2[0000-0001-5109-3700-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0001-5109-3700-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005991050002194243, 'start': 1685951451.6698408, 'stop': 1685951451.670441, '$report_type': 'TestReport', 'item_index': 543, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0001-5109-3700-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0001-5109-3700-True]'), 'keywords': {'test_check_mod_11_2[0000-0001-5109-3700-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0001-5109-3700-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000389791000088735, 'start': 1685951451.6708689, 'stop': 1685951451.6712599, '$report_type': 'TestReport', 'item_index': 543, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0001-5109-3700-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0001-5109-3700-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0002-1694-233X-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1694-233X-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1694-233X-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1694-233X-True]'), 'keywords': {'test_check_mod_11_2[0000-0002-1694-233X-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1694-233X-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000836033999803476, 'start': 1685951451.672786, 'stop': 1685951451.673625, '$report_type': 'TestReport', 'item_index': 544, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1694-233X-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1694-233X-True]'), 'keywords': {'test_check_mod_11_2[0000-0002-1694-233X-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1694-233X-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004369629996290314, 'start': 1685951451.6747231, 'stop': 1685951451.6751628, '$report_type': 'TestReport', 'item_index': 544, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1694-233X-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1694-233X-True]'), 'keywords': {'test_check_mod_11_2[0000-0002-1694-233X-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1694-233X-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002847200003088801, 'start': 1685951451.675647, 'stop': 1685951451.675933, '$report_type': 'TestReport', 'item_index': 544, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0002-1694-233X-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1694-233X-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000000218250097-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000000218250097-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000000218250097-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000000218250097-True]'), 'keywords': {'test_check_mod_11_2[0000000218250097-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000000218250097-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005957249995844904, 'start': 1685951451.676773, 'stop': 1685951451.6773708, '$report_type': 'TestReport', 'item_index': 545, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000000218250097-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000000218250097-True]'), 'keywords': {'test_check_mod_11_2[0000000218250097-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000000218250097-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00040506300047127297, 'start': 1685951451.6781828, 'stop': 1685951451.6785889, '$report_type': 'TestReport', 'item_index': 545, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000000218250097-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000000218250097-True]'), 'keywords': {'test_check_mod_11_2[0000000218250097-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000000218250097-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004069939996043104, 'start': 1685951451.67916, 'stop': 1685951451.679569, '$report_type': 'TestReport', 'item_index': 545, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000000218250097-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000000218250097-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000000151093700-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000000151093700-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000000151093700-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000000151093700-True]'), 'keywords': {'test_check_mod_11_2[0000000151093700-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000000151093700-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008713150000403402, 'start': 1685951451.680701, 'stop': 1685951451.6815739, '$report_type': 'TestReport', 'item_index': 546, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000000151093700-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000000151093700-True]'), 'keywords': {'test_check_mod_11_2[0000000151093700-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000000151093700-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00034062399936374277, 'start': 1685951451.682168, 'stop': 1685951451.6825101, '$report_type': 'TestReport', 'item_index': 546, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000000151093700-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000000151093700-True]'), 'keywords': {'test_check_mod_11_2[0000000151093700-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000000151093700-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004202109994366765, 'start': 1685951451.682956, 'stop': 1685951451.6833768, '$report_type': 'TestReport', 'item_index': 546, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000000151093700-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000000151093700-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[000000021694233X-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[000000021694233X-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[000000021694233X-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[000000021694233X-True]'), 'keywords': {'test_check_mod_11_2[000000021694233X-True]': 1, 'parametrize': 1, 'pytestmark': 1, '000000021694233X-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005415870000433642, 'start': 1685951451.684496, 'stop': 1685951451.685039, '$report_type': 'TestReport', 'item_index': 547, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[000000021694233X-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[000000021694233X-True]'), 'keywords': {'test_check_mod_11_2[000000021694233X-True]': 1, 'parametrize': 1, 'pytestmark': 1, '000000021694233X-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002540040004532784, 'start': 1685951451.685647, 'stop': 1685951451.685902, '$report_type': 'TestReport', 'item_index': 547, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[000000021694233X-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[000000021694233X-True]'), 'keywords': {'test_check_mod_11_2[000000021694233X-True]': 1, 'parametrize': 1, 'pytestmark': 1, '000000021694233X-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003871489998346078, 'start': 1685951451.6862578, 'stop': 1685951451.686647, '$report_type': 'TestReport', 'item_index': 547, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[000000021694233X-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[000000021694233X-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0002-1694-233X-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0002-1694-233X-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0002-1694-233X-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0002-1694-233X-True]'), 'keywords': {'test_check_mod_11_2[0002-1694-233X-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0002-1694-233X-True': 1, 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{'test_check_mod_11_2[0002-1694-233X-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0002-1694-233X-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003969079998569214, 'start': 1685951451.688991, 'stop': 1685951451.6893902, '$report_type': 'TestReport', 'item_index': 548, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0002-1694-233X-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0002-1694-233X-True]'), 'keywords': {'test_check_mod_11_2[0002-1694-233X-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0002-1694-233X-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005645410001307027, 'start': 1685951451.689879, 'stop': 1685951451.6904461, '$report_type': 'TestReport', 'item_index': 548, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0002-1694-233X-True] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0002-1694-233X-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-009X-False] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-009X-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-009X-False]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-009X-False]'), 'keywords': {'test_check_mod_11_2[0000-0002-1825-009X-False]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-009X-False': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000769929999478336, 'start': 1685951451.691948, 'stop': 1685951451.6927202, '$report_type': 'TestReport', 'item_index': 549, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-009X-False]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-009X-False]'), 'keywords': {'test_check_mod_11_2[0000-0002-1825-009X-False]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-009X-False': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004110870004296885, 'start': 1685951451.6934688, 'stop': 1685951451.6938822, '$report_type': 'TestReport', 'item_index': 549, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-009X-False]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-009X-False]'), 'keywords': {'test_check_mod_11_2[0000-0002-1825-009X-False]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-009X-False': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003589179996197345, 'start': 1685951451.694466, 'stop': 1685951451.694827, '$report_type': 'TestReport', 'item_index': 549, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-009X-False] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-009X-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0001-5109-3707-False] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0001-5109-3707-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0001-5109-3707-False]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0001-5109-3707-False]'), 'keywords': {'test_check_mod_11_2[0000-0001-5109-3707-False]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0001-5109-3707-False': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008409189995290944, 'start': 1685951451.696099, 'stop': 1685951451.6969411, '$report_type': 'TestReport', 'item_index': 550, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0001-5109-3707-False]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0001-5109-3707-False]'), 'keywords': {'test_check_mod_11_2[0000-0001-5109-3707-False]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0001-5109-3707-False': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00033397400056855986, 'start': 1685951451.697494, 'stop': 1685951451.69783, '$report_type': 'TestReport', 'item_index': 550, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0001-5109-3707-False]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0001-5109-3707-False]'), 'keywords': {'test_check_mod_11_2[0000-0001-5109-3707-False]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0001-5109-3707-False': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005488080005306983, 'start': 1685951451.698357, 'stop': 1685951451.698907, '$report_type': 'TestReport', 'item_index': 550, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0001-5109-3707-False] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0001-5109-3707-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0002-1694-2330-False] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1694-2330-False]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1694-2330-False]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1694-2330-False]'), 'keywords': {'test_check_mod_11_2[0000-0002-1694-2330-False]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1694-2330-False': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014147149995551445, 'start': 1685951451.700108, 'stop': 1685951451.701525, '$report_type': 'TestReport', 'item_index': 551, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1694-2330-False]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1694-2330-False]'), 'keywords': {'test_check_mod_11_2[0000-0002-1694-2330-False]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1694-2330-False': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005379149997679633, 'start': 1685951451.702265, 'stop': 1685951451.7028039, '$report_type': 'TestReport', 'item_index': 551, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + 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'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "график",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to 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script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp44oq2voa\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp44oq2voa\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7918996069993227, 'start': 1685951450.9114509, 'stop': 1685951451.7033339, '$report_type': 'TestReport', 'item_index': 506, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_runtest_logreport --> [] [hook] + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0002-1694-2330-False] + location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1694-2330-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011373939996701665, 'start': 1685951451.705606, 'stop': 1685951451.706746, '$report_type': 'TestReport', 'item_index': 552, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]'), 'keywords': {'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "график",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp44oq2voa\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp44oq2voa\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0011550549997991766, 'start': 1685951451.705198, 'stop': 1685951451.7063549, '$report_type': 'TestReport', 'item_index': 506, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0014078220001465525, 'start': 1685951451.707592, 'stop': 1685951451.709002, '$report_type': 'TestReport', 'item_index': 552, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003332229998704861, 'start': 1685951451.7095811, 'stop': 1685951451.7099159, '$report_type': 'TestReport', 'item_index': 552, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]'), 'keywords': {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0022639859998889733, 'start': 1685951451.709167, 'stop': 1685951451.711433, '$report_type': 'TestReport', 'item_index': 507, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 745, 'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]') + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007346430002144189, 'start': 1685951451.711381, 'stop': 1685951451.712117, '$report_type': 'TestReport', 'item_index': 553, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003641949997472693, 'start': 1685951451.712659, 'stop': 1685951451.713024, '$report_type': 'TestReport', 'item_index': 553, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002946350005004206, 'start': 1685951451.713682, 'stop': 1685951451.713978, '$report_type': 'TestReport', 'item_index': 553, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 745, 'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097] + location: ('tests/test_provenance.py', 745, 'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]'), 'keywords': {'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00045533299999078736, 'start': 1685951451.714863, 'stop': 1685951451.7153192, '$report_type': 'TestReport', 'item_index': 554, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]'), 'keywords': {'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00032317899967893027, 'start': 1685951451.716031, 'stop': 1685951451.716356, '$report_type': 'TestReport', 'item_index': 554, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]'), 'keywords': {'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00027228799990552943, 'start': 1685951451.716735, 'stop': 1685951451.7170088, '$report_type': 'TestReport', 'item_index': 554, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097] + location: ('tests/test_provenance.py', 745, 'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw3] received command runtests {'indices': [557, 558, 559, 560]}\n")], 'duration': 0.0010702509998736787, 'start': 1685951451.718146, 'stop': 1685951451.7192168, '$report_type': 'TestReport', 'item_index': 555, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw3] received command runtests {'indices': [557, 558, 559, 560]}\n")], 'duration': 0.00044140499994682614, 'start': 1685951451.719826, 'stop': 1685951451.720269, '$report_type': 'TestReport', 'item_index': 555, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw3] received command runtests {'indices': [557, 558, 559, 560]}\n")], 'duration': 0.00029204699967522174, 'start': 1685951451.720681, 'stop': 1685951451.7209752, '$report_type': 'TestReport', 'item_index': 555, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 745, 'test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008047190003708238, 'start': 1685951451.722572, 'stop': 1685951451.723379, '$report_type': 'TestReport', 'item_index': 556, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005485689998749876, 'start': 1685951451.72414, 'stop': 1685951451.724691, '$report_type': 'TestReport', 'item_index': 556, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00041454499933024636, 'start': 1685951451.7256389, 'stop': 1685951451.726055, '$report_type': 'TestReport', 'item_index': 556, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 745, 'test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[0002-1694-2332] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[0002-1694-2332]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[0002-1694-2332]'), 'keywords': {'test_invalid_orcid[0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, '0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00042271599977539154, 'start': 1685951451.727045, 'stop': 1685951451.727469, '$report_type': 'TestReport', 'item_index': 557, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[0002-1694-2332]'), 'keywords': {'test_invalid_orcid[0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, '0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00039211800049088197, 'start': 1685951451.7279549, 'stop': 1685951451.728348, '$report_type': 'TestReport', 'item_index': 557, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[0002-1694-2332]'), 'keywords': {'test_invalid_orcid[0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, '0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00033168800018756883, 'start': 1685951451.728999, 'stop': 1685951451.729332, '$report_type': 'TestReport', 'item_index': 557, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[0002-1694-2332] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[0002-1694-2332]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[https://orcid.org/0000-0002-1694-2332] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]'), 'keywords': {'test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00043069900038972264, 'start': 1685951451.730485, 'stop': 1685951451.7309172, '$report_type': 'TestReport', 'item_index': 558, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]'), 'keywords': {'test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002679489998627105, 'start': 1685951451.731301, 'stop': 1685951451.73157, '$report_type': 'TestReport', 'item_index': 558, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]'), 'keywords': {'test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002993910002260236, 'start': 1685951451.732289, 'stop': 1685951451.7325902, '$report_type': 'TestReport', 'item_index': 558, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[https://orcid.org/0000-0002-1694-2332] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[0000-0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[0000-0002-1694-2332]'), 'keywords': {'test_invalid_orcid[0000-0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003274829996371409, 'start': 1685951451.733471, 'stop': 1685951451.7338, '$report_type': 'TestReport', 'item_index': 559, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[0000-0002-1694-2332] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[0000-0002-1694-2332]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[0000-0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[0000-0002-1694-2332]'), 'keywords': {'test_invalid_orcid[0000-0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005299230006130529, 'start': 1685951451.73413, 'stop': 1685951451.734661, '$report_type': 'TestReport', 'item_index': 559, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[0000-0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[0000-0002-1694-2332]'), 'keywords': {'test_invalid_orcid[0000-0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002615349994812277, 'start': 1685951451.735347, 'stop': 1685951451.735609, '$report_type': 'TestReport', 'item_index': 559, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[0000-0002-1694-2332] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[0000-0002-1694-2332]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[https://orcid.org/000000021694233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/000000021694233X]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org/000000021694233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/000000021694233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org/000000021694233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/000000021694233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003034880000996054, 'start': 1685951451.7363992, 'stop': 1685951451.736703, '$report_type': 'TestReport', 'item_index': 560, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org/000000021694233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/000000021694233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org/000000021694233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/000000021694233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00024056900019786553, 'start': 1685951451.73705, 'stop': 1685951451.737292, '$report_type': 'TestReport', 'item_index': 560, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org/000000021694233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/000000021694233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org/000000021694233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/000000021694233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002578959993115859, 'start': 1685951451.737841, 'stop': 1685951451.7381, '$report_type': 'TestReport', 'item_index': 560, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[https://orcid.org/000000021694233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/000000021694233X]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[000000021694233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[000000021694233X]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[000000021694233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[000000021694233X]'), 'keywords': {'test_invalid_orcid[000000021694233X]': 1, 'parametrize': 1, 'pytestmark': 1, '000000021694233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005018640003982, 'start': 1685951451.7391071, 'stop': 1685951451.739611, '$report_type': 'TestReport', 'item_index': 561, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[000000021694233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[000000021694233X]'), 'keywords': {'test_invalid_orcid[000000021694233X]': 1, 'parametrize': 1, 'pytestmark': 1, '000000021694233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00044499599971459247, 'start': 1685951451.7400498, 'stop': 1685951451.740496, '$report_type': 'TestReport', 'item_index': 561, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[000000021694233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[000000021694233X]'), 'keywords': {'test_invalid_orcid[000000021694233X]': 1, 'parametrize': 1, 'pytestmark': 1, '000000021694233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00046694299999217037, 'start': 1685951451.7413929, 'stop': 1685951451.7418618, '$report_type': 'TestReport', 'item_index': 561, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[000000021694233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[000000021694233X]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[https://example.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://example.org/0000-0002-1694-233X]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://example.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://example.org/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[https://example.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://example.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004732390007120557, 'start': 1685951451.743167, 'stop': 1685951451.7436411, '$report_type': 'TestReport', 'item_index': 562, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://example.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://example.org/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[https://example.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://example.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00036202600040269317, 'start': 1685951451.744191, 'stop': 1685951451.744554, '$report_type': 'TestReport', 'item_index': 562, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://example.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://example.org/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[https://example.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://example.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00025080300019908464, 'start': 1685951451.7451782, 'stop': 1685951451.74543, '$report_type': 'TestReport', 'item_index': 562, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[https://example.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://example.org/0000-0002-1694-233X]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'ftp://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002909930008172523, 'start': 1685951451.7472482, 'stop': 1685951451.74754, '$report_type': 'TestReport', 'item_index': 563, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'ftp://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004054629998790915, 'start': 1685951451.748232, 'stop': 1685951451.748638, '$report_type': 'TestReport', 'item_index': 563, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org:443/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00045285899977898225, 'start': 1685951451.7498848, 'stop': 1685951451.750339, '$report_type': 'TestReport', 'item_index': 564, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org:443/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002515780006433488, 'start': 1685951451.750687, 'stop': 1685951451.750939, '$report_type': 'TestReport', 'item_index': 564, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] +[hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file-file_dir1-expected1]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file-file_dir1-expected1]'), 'keywords': {'test_normalizeFilesDirs[file-file_dir1-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, 'file-file_dir1-expected1': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004152450001129182, 'start': 1685951448.650466, 'stop': 1685951448.650882, '$report_type': 'TestReport', 'item_index': 514, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org:443/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003813679995801067, 'start': 1685951451.751585, 'stop': 1685951451.751968, '$report_type': 'TestReport', 'item_index': 564, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org:80/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004132009999011643, 'start': 1685951451.752942, 'stop': 1685951451.7533572, '$report_type': 'TestReport', 'item_index': 565, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org:80/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006339709998428589, 'start': 1685951451.753885, 'stop': 1685951451.7545211, '$report_type': 'TestReport', 'item_index': 565, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org:80/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003594289992179256, 'start': 1685951451.7551591, 'stop': 1685951451.75552, '$report_type': 'TestReport', 'item_index': 565, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[]'), 'keywords': {'test_invalid_orcid[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006703340004605707, 'start': 1685951451.757062, 'stop': 1685951451.757735, '$report_type': 'TestReport', 'item_index': 566, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[]'), 'keywords': {'test_invalid_orcid[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003938019999623066, 'start': 1685951451.758364, 'stop': 1685951451.75876, '$report_type': 'TestReport', 'item_index': 566, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[]'), 'keywords': {'test_invalid_orcid[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003428029995120596, 'start': 1685951451.759594, 'stop': 1685951451.759939, '$report_type': 'TestReport', 'item_index': 566, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_invalid_orcid[] + location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_whoami + location: ('tests/test_provenance.py', 777, 'test_whoami') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_whoami', 'location': ('tests/test_provenance.py', 777, 'test_whoami'), 'keywords': {'test_whoami': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002886559996113647, 'start': 1685951451.760962, 'stop': 1685951451.7612522, '$report_type': 'TestReport', 'item_index': 567, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_whoami', 'location': ('tests/test_provenance.py', 777, 'test_whoami'), 'keywords': {'test_whoami': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0029586099999505677, 'start': 1685951451.761823, 'stop': 1685951451.7647831, '$report_type': 'TestReport', 'item_index': 567, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_whoami', 'location': ('tests/test_provenance.py', 777, 'test_whoami'), 'keywords': {'test_whoami': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00024329300049430458, 'start': 1685951451.765263, 'stop': 1685951451.7655082, '$report_type': 'TestReport', 'item_index': 567, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_whoami + location: ('tests/test_provenance.py', 777, 'test_whoami') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_research_object + location: ('tests/test_provenance.py', 783, 'test_research_object') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_research_object', 'location': ('tests/test_provenance.py', 783, 'test_research_object'), 'keywords': {'test_research_object': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00024808000034681754, 'start': 1685951451.7682009, 'stop': 1685951451.768451, '$report_type': 'TestReport', 'item_index': 568, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_research_object', 'location': ('tests/test_provenance.py', 783, 'test_research_object'), 'keywords': {'test_research_object': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00037334899934649, 'start': 1685951451.7691488, 'stop': 1685951451.7695239, '$report_type': 'TestReport', 'item_index': 568, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_research_object', 'location': ('tests/test_provenance.py', 783, 'test_research_object'), 'keywords': {'test_research_object': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00030079200041654985, 'start': 1685951451.770102, 'stop': 1685951451.770405, '$report_type': 'TestReport', 'item_index': 568, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_research_object + location: ('tests/test_provenance.py', 783, 'test_research_object') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_research_object_picklability + location: ('tests/test_provenance.py', 788, 'test_research_object_picklability') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_research_object_picklability', 'location': ('tests/test_provenance.py', 788, 'test_research_object_picklability'), 'keywords': {'test_research_object_picklability': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj')], 'duration': 0.023298113999771886, 'start': 1685951451.772306, 'stop': 1685951451.795605, '$report_type': 'TestReport', 'item_index': 569, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_research_object_picklability', 'location': ('tests/test_provenance.py', 788, 'test_research_object_picklability'), 'keywords': {'test_research_object_picklability': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj')], 'duration': 0.0006209909997778595, 'start': 1685951451.796177, 'stop': 1685951451.796799, '$report_type': 'TestReport', 'item_index': 569, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_research_object_picklability', 'location': ('tests/test_provenance.py', 788, 'test_research_object_picklability'), 'keywords': {'test_research_object_picklability': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj')], 'duration': 0.00234540899964486, 'start': 1685951451.797377, 'stop': 1685951451.799724, '$report_type': 'TestReport', 'item_index': 569, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_research_object_picklability + location: ('tests/test_provenance.py', 788, 'test_research_object_picklability') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_directory_workflow_no_listing + location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow_no_listing', 'location': ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing'), 'keywords': {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016229729999395204, 'start': 1685951451.801435, 'stop': 1685951451.80306, '$report_type': 'TestReport', 'item_index': 570, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]'), 'keywords': {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/%F0%92%81%83",\n "basename": "ð’ƒ",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmppaqyosg7\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppaqyosg7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7048519689997192, 'start': 1685951451.7120519, 'stop': 1685951452.416888, '$report_type': 'TestReport', 'item_index': 507, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]'), 'keywords': {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/%F0%92%81%83",\n "basename": "ð’ƒ",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmppaqyosg7\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppaqyosg7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006576920004590647, 'start': 1685951452.418154, 'stop': 1685951452.418813, '$report_type': 'TestReport', 'item_index': 507, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0023664050004299497, 'start': 1685951452.4210129, 'stop': 1685951452.423381, '$report_type': 'TestReport', 'item_index': 508, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_parallel.py::test_sequential_workflow', 'location': ('tests/test_parallel.py', 10, 'test_sequential_workflow'), 'keywords': {'test_sequential_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] inputs {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] start\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] starting step step1_3\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1_3\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_3), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1_3] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1,target=/GbFKKR \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/5jjsgruc/20230605095051-246049.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt > /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] Max memory used: 0MiB\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] outputs {\n "output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] Removing input staging directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/hklbq548\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] Removing temporary directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] starting step step2_3\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step2_3] start\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step2_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] outputs {\n "count_output": 16\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fqocvrn2\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _5] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _5] inputs {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:610 [workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\nINFO cwltool:workflow_job.py:765 [workflow _5] start\nINFO cwltool:workflow_job.py:613 [workflow _5] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_3), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:610 [workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1_3] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1_3] /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1,target=/GbFKKR \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/5jjsgruc/20230605095051-246049.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt > /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output\nINFO cwltool:job.py:905 [job step1_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/hklbq548\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb\nINFO cwltool:workflow_job.py:613 [workflow _5] starting step step2_3\nDEBUG cwltool:workflow_job.py:727 [step step2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_3] start\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:564 [step step2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _5] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fqocvrn2')], 'duration': 1.3139026039998498, 'start': 1685951451.118825, 'stop': 1685951452.432698, '$report_type': 'TestReport', 'item_index': 494, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_parallel.py::test_sequential_workflow', 'location': ('tests/test_parallel.py', 10, 'test_sequential_workflow'), 'keywords': {'test_sequential_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] inputs {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] start\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] starting step step1_3\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1_3\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_3), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1_3] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1,target=/GbFKKR \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/5jjsgruc/20230605095051-246049.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt > /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] Max memory used: 0MiB\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] outputs {\n "output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] Removing input staging directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/hklbq548\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] Removing temporary directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] starting step step2_3\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step2_3] start\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step2_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] outputs {\n "count_output": 16\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fqocvrn2\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _5] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _5] inputs {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:610 [workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\nINFO cwltool:workflow_job.py:765 [workflow _5] start\nINFO cwltool:workflow_job.py:613 [workflow _5] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_3), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:610 [workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1_3] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1_3] /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1,target=/GbFKKR \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/5jjsgruc/20230605095051-246049.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt > /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output\nINFO cwltool:job.py:905 [job step1_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/hklbq548\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb\nINFO cwltool:workflow_job.py:613 [workflow _5] starting step step2_3\nDEBUG cwltool:workflow_job.py:727 [step step2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_3] start\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:564 [step step2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _5] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fqocvrn2')], 'duration': 0.000757715999498032, 'start': 1685951452.434391, 'stop': 1685951452.4351501, '$report_type': 'TestReport', 'item_index': 494, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_parallel.py::test_sequential_workflow + location: ('tests/test_parallel.py', 10, 'test_sequential_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_parallel.py::test_scattered_workflow', 'location': ('tests/test_parallel.py', 23, 'test_scattered_workflow'), 'keywords': {'test_scattered_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002563279995229095, 'start': 1685951452.436842, 'stop': 1685951452.437099, '$report_type': 'TestReport', 'item_index': 495, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_parallel.py::test_scattered_workflow + location: ('tests/test_parallel.py', 23, 'test_scattered_workflow') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_hello_workflow', 'location': ('tests/test_provenance.py', 49, 'test_hello_workflow'), 'keywords': {'test_hello_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "response": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt",\n "basename": "response.txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl --usermessage Hello workflow\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpglr7rc0q/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step0_4\n\x1b[1;30mINFO\x1b[0m [step step0_4] start\n\x1b[1;30mINFO\x1b[0m [job step0_4] /private/tmp/docker_tmpky30xwh8$ echo \\\n -n \\\n -e \\\n 'Hello workflow' > /private/tmp/docker_tmpky30xwh8/response.txt\n\x1b[1;30mINFO\x1b[0m [job step0_4] completed success\n\x1b[1;30mINFO\x1b[0m [step step0_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl --usermessage Hello workflow\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\', job_order=[\'--usermessage\', \'Hello workflow\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 327fe927e223c88dca78a0ea5105c922f0fba00b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 60f0e978a2ac9c4ef469177fbe58189c76d2dd6b39c5c6b660c5ecb3ccd3d2a4 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: ab665a7342ac208014e8bcb016f5643a0cbc1cc5f45595616f992dbd30e3b98324bca187d0fec8ef4f5a9de604932b3caf0fe61771af4baeea9a3d946ae2fefd workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpglr7rc0q/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl",\n "usermessage": "Hello workflow"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'usermessage\': \'Hello workflow\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello workflow\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: d4facb14439b8696b380c65f8efc92e00bffbfa2 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: cea82f27619ef873390bbd420bc76eaf38ff6428f3bdc3e0decb7b915885e1ce workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: feab70d27d2c04c33d6fad2eebf6476963a889161fb4664d48aeeacbc1954d14c73d1be159b8b14bb5bee6568ea24a2a34eaa5442216bfbafdac08304a6e43e3 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/manifest-sha1.txt: 260807aefd9032a48a0d88d4ff7110a5bbfaea3d data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "usermessage": "Hello workflow"\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step0_4\nDEBUG cwltool:workflow_job.py:727 [step step0_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/message": "Hello workflow"\n}\nDEBUG cwltool:workflow_job.py:732 [step step0_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/message": "Hello workflow"\n}\nINFO cwltool:workflow_job.py:75 [step step0_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step0_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/78eec50f-a8c4-49ef-b819-b3549af9288a as part of step step0_4\nDEBUG cwltool:command_line_tool.py:988 [job step0_4] {\n "message": "Hello workflow"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step0_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step0_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-e"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello workflow"\n }\n]\nDEBUG cwltool:job.py:215 [job step0_4] initial work dir {}\nINFO cwltool:job.py:266 [job step0_4] /private/tmp/docker_tmpky30xwh8$ echo \\\n -n \\\n -e \\\n \'Hello workflow\' > /private/tmp/docker_tmpky30xwh8/response.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/manifest-sha1.txt: ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nINFO cwltool:job.py:419 [job step0_4] completed success\nDEBUG cwltool:job.py:422 [job step0_4] outputs {\n "response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step0_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nINFO cwltool:workflow_job.py:572 [step step0_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nDEBUG cwltool:job.py:446 [job step0_4] Removing input staging directory /private/tmp/docker_tmphlf_rba8\nDEBUG cwltool:job.py:454 [job step0_4] Removing temporary directory /private/tmp/docker_tmp7h1158q7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpky30xwh8/response.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfkeo19kl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpky30xwh8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: efb0801b16087469a4510229b16bfcff66750932 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 2230d4ebababf075d8fbc7e04f19411178b0b594711eff698a6da6084e19f480 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 1a3847b8bc1ae8ffecfc640d7a473975d5b1e216830043bd6a98aec214ddd9a4b01e979fa7111dbd4936aa1390a0498e6e9169b965317424d4e70a4d63f45e6a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 9b771bb6461f656650a1bfb6000ea190b1bddd35 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: d41f4929fa8d97fafc3b2034e3bbd869bc05803a137b70afa382c8e3661646dc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: aa49365eaeb9437311c0aa2b912741047a21ba9c44f7e0ef7c88c0c700921ff4c909e7655ebb793b0b83d9a546058b7cb7647867c69e372b1d41bb6290fef3f8 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 90441e825ca65d0df8ce3b48c504a2e973bceef9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: f0e7a69d8bc9bfac7979e0e9acbf945b4e8e5d0056d02a0f25e0d693fdd57488 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: a0f1727b0560d4bf9ec294531561cef5775ebee76ee71de7fff3027a47170c9992538c9a00853663ace4ade59bbc09886a7018c62a9f9436753d460a28ffd98b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 9a0f27052dd2175caf2a67758f7691746e41ccd2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 1a8c28680fbb8bac16231a866740bbaeb15581e14a9377ff970b5e85c89999fc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: e65b6e2a1abcb2d07d64e5680662c38a4bffc93ed129a4c704e53229ffbed61895d5687b6ac94d786616db330f1afbd3782c8574812633500833f9607b210d25 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 1ad236bd4b38764eda7811f98521099ffb363ecc metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 0c6df5b09f2c2a7e8f9608a5764566395bad043ca95ca93a6cedf92f2c799e0e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 969f2cf9ed709f655ee14e64530bc5fb2b09a6658bc66ad71b0656f870b55eb702e2a9f5a5583174fdb9a9d4d20e8f7125b35c731dd63ff39b8878de2b0023cf metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 189f0652a59dbaa89976f6b3f9d8257ef9d098ea metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 518d054df5fb1de9a011e6bff56ac8a1bef2feab49691f4db926372c49019f7a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 21f81b0d457e735d55dce20c5388f10ec251bf2e228ffbee2c4ac221c6449998f0adef0ce764361381d4ac73ad9907b4eeaf32d82426c254c4c9a579b5fbd3aa metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'response\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\', \'basename\': \'response.txt\', \'nameroot\': \'response\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\', \'size\': 17, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\', \'basename\': \'response.txt\', \'nameroot\': \'response\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\', \'size\': 17, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: response.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: response\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 17\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 618f86915ea9700ecb3b704795a4ae85bf643425 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 8ac22a6c1cabae7deb3b29b0e2bda23e71052570143f0acbf2a09da703487dca workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: cf6d7a5f6330db6c0e0852718916891cc1444442f31cd4cfbba37b618d91f92004d2596775718de660ae2532c587e013c37ed7e795796cdc8ed34d0899661322 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: e1fc01826e8384fb32a1064690707df6334017bb snapshot/hello-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 01d934f8701a6367ebb2d2e1ec8834d6da95f348521dba8612633e4be6252965 snapshot/hello-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: d75bcdacf77bb436846d87bf6cbb243d7720a2bc1b3b165e6558df9a82ebdde0baea7a5ae91afebd85fc3e0ad3165f1523ea73a409b46f86ee6c7385a6b647d3 snapshot/hello-workflow.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 555f09620cd5b296ed8407059a0f2357ea0bb092 metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: ac58b85e9b87b81165c5fc2f3739964d2666cefada2b344661084a7e5218341e metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 001951b3906ae97db9f6bd8dec485bb4563f70697ed163e0521bdec155d0b7e9223019c1a0525300708ee55653cba9a80c2e0edae23fff7bbac807811bbbc236 metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 8d7b3a5c56948366a29ee377680d0ac38129de05 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 23801bfbbba411f431e6b84bf181dc5514967c8e824f82728e70a2fda8be11ce metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 2671f6b2e92069ea01f98c638d4e5eb042aee0b59619147d2925f3603a504581fc874f715a039897175a5f63b3f1acb6f662a0ab488a4e000b797c5ea53a6d45 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 5f3f3974d5347536a098f33eb55826382755b5a8 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 05b4f6a002ef3f090d70b6ade829ca1bf679eac0abe89707ca5ccf3d6d74b193 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: b424ef8f2d9859451976287a408004919705b84b3bc642e1e877560d117acefdd7ea5431438decfcb8e3bc24c5d758156005b869df64c4dfffefa29e9559c60a bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance')], 'duration': 1.1406687319995399, 'start': 1685951451.628845, 'stop': 1685951452.7694871, '$report_type': 'TestReport', 'item_index': 523, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_hello_workflow', 'location': ('tests/test_provenance.py', 49, 'test_hello_workflow'), 'keywords': {'test_hello_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "response": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt",\n "basename": "response.txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl --usermessage Hello workflow\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpglr7rc0q/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step0_4\n\x1b[1;30mINFO\x1b[0m [step step0_4] start\n\x1b[1;30mINFO\x1b[0m [job step0_4] /private/tmp/docker_tmpky30xwh8$ echo \\\n -n \\\n -e \\\n 'Hello workflow' > /private/tmp/docker_tmpky30xwh8/response.txt\n\x1b[1;30mINFO\x1b[0m [job step0_4] completed success\n\x1b[1;30mINFO\x1b[0m [step step0_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl --usermessage Hello workflow\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\', job_order=[\'--usermessage\', \'Hello workflow\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 327fe927e223c88dca78a0ea5105c922f0fba00b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 60f0e978a2ac9c4ef469177fbe58189c76d2dd6b39c5c6b660c5ecb3ccd3d2a4 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: ab665a7342ac208014e8bcb016f5643a0cbc1cc5f45595616f992dbd30e3b98324bca187d0fec8ef4f5a9de604932b3caf0fe61771af4baeea9a3d946ae2fefd workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpglr7rc0q/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl",\n "usermessage": "Hello workflow"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'usermessage\': \'Hello workflow\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello workflow\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: d4facb14439b8696b380c65f8efc92e00bffbfa2 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: cea82f27619ef873390bbd420bc76eaf38ff6428f3bdc3e0decb7b915885e1ce workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: feab70d27d2c04c33d6fad2eebf6476963a889161fb4664d48aeeacbc1954d14c73d1be159b8b14bb5bee6568ea24a2a34eaa5442216bfbafdac08304a6e43e3 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/manifest-sha1.txt: 260807aefd9032a48a0d88d4ff7110a5bbfaea3d data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "usermessage": "Hello workflow"\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step0_4\nDEBUG cwltool:workflow_job.py:727 [step step0_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/message": "Hello workflow"\n}\nDEBUG cwltool:workflow_job.py:732 [step step0_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/message": "Hello workflow"\n}\nINFO cwltool:workflow_job.py:75 [step step0_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step0_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/78eec50f-a8c4-49ef-b819-b3549af9288a as part of step step0_4\nDEBUG cwltool:command_line_tool.py:988 [job step0_4] {\n "message": "Hello workflow"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step0_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step0_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-e"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello workflow"\n }\n]\nDEBUG cwltool:job.py:215 [job step0_4] initial work dir {}\nINFO cwltool:job.py:266 [job step0_4] /private/tmp/docker_tmpky30xwh8$ echo \\\n -n \\\n -e \\\n \'Hello workflow\' > /private/tmp/docker_tmpky30xwh8/response.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/manifest-sha1.txt: ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nINFO cwltool:job.py:419 [job step0_4] completed success\nDEBUG cwltool:job.py:422 [job step0_4] outputs {\n "response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step0_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nINFO cwltool:workflow_job.py:572 [step step0_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nDEBUG cwltool:job.py:446 [job step0_4] Removing input staging directory /private/tmp/docker_tmphlf_rba8\nDEBUG cwltool:job.py:454 [job step0_4] Removing temporary directory /private/tmp/docker_tmp7h1158q7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpky30xwh8/response.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfkeo19kl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpky30xwh8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: efb0801b16087469a4510229b16bfcff66750932 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 2230d4ebababf075d8fbc7e04f19411178b0b594711eff698a6da6084e19f480 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 1a3847b8bc1ae8ffecfc640d7a473975d5b1e216830043bd6a98aec214ddd9a4b01e979fa7111dbd4936aa1390a0498e6e9169b965317424d4e70a4d63f45e6a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 9b771bb6461f656650a1bfb6000ea190b1bddd35 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: d41f4929fa8d97fafc3b2034e3bbd869bc05803a137b70afa382c8e3661646dc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: aa49365eaeb9437311c0aa2b912741047a21ba9c44f7e0ef7c88c0c700921ff4c909e7655ebb793b0b83d9a546058b7cb7647867c69e372b1d41bb6290fef3f8 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 90441e825ca65d0df8ce3b48c504a2e973bceef9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: f0e7a69d8bc9bfac7979e0e9acbf945b4e8e5d0056d02a0f25e0d693fdd57488 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: a0f1727b0560d4bf9ec294531561cef5775ebee76ee71de7fff3027a47170c9992538c9a00853663ace4ade59bbc09886a7018c62a9f9436753d460a28ffd98b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 9a0f27052dd2175caf2a67758f7691746e41ccd2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 1a8c28680fbb8bac16231a866740bbaeb15581e14a9377ff970b5e85c89999fc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: e65b6e2a1abcb2d07d64e5680662c38a4bffc93ed129a4c704e53229ffbed61895d5687b6ac94d786616db330f1afbd3782c8574812633500833f9607b210d25 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 1ad236bd4b38764eda7811f98521099ffb363ecc metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 0c6df5b09f2c2a7e8f9608a5764566395bad043ca95ca93a6cedf92f2c799e0e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 969f2cf9ed709f655ee14e64530bc5fb2b09a6658bc66ad71b0656f870b55eb702e2a9f5a5583174fdb9a9d4d20e8f7125b35c731dd63ff39b8878de2b0023cf metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 189f0652a59dbaa89976f6b3f9d8257ef9d098ea metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 518d054df5fb1de9a011e6bff56ac8a1bef2feab49691f4db926372c49019f7a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 21f81b0d457e735d55dce20c5388f10ec251bf2e228ffbee2c4ac221c6449998f0adef0ce764361381d4ac73ad9907b4eeaf32d82426c254c4c9a579b5fbd3aa metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'response\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\', \'basename\': \'response.txt\', \'nameroot\': \'response\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\', \'size\': 17, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\', \'basename\': \'response.txt\', \'nameroot\': \'response\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\', \'size\': 17, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: response.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: response\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 17\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 618f86915ea9700ecb3b704795a4ae85bf643425 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 8ac22a6c1cabae7deb3b29b0e2bda23e71052570143f0acbf2a09da703487dca workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: cf6d7a5f6330db6c0e0852718916891cc1444442f31cd4cfbba37b618d91f92004d2596775718de660ae2532c587e013c37ed7e795796cdc8ed34d0899661322 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: e1fc01826e8384fb32a1064690707df6334017bb snapshot/hello-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 01d934f8701a6367ebb2d2e1ec8834d6da95f348521dba8612633e4be6252965 snapshot/hello-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: d75bcdacf77bb436846d87bf6cbb243d7720a2bc1b3b165e6558df9a82ebdde0baea7a5ae91afebd85fc3e0ad3165f1523ea73a409b46f86ee6c7385a6b647d3 snapshot/hello-workflow.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 555f09620cd5b296ed8407059a0f2357ea0bb092 metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: ac58b85e9b87b81165c5fc2f3739964d2666cefada2b344661084a7e5218341e metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 001951b3906ae97db9f6bd8dec485bb4563f70697ed163e0521bdec155d0b7e9223019c1a0525300708ee55653cba9a80c2e0edae23fff7bbac807811bbbc236 metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 8d7b3a5c56948366a29ee377680d0ac38129de05 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 23801bfbbba411f431e6b84bf181dc5514967c8e824f82728e70a2fda8be11ce metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 2671f6b2e92069ea01f98c638d4e5eb042aee0b59619147d2925f3603a504581fc874f715a039897175a5f63b3f1acb6f662a0ab488a4e000b797c5ea53a6d45 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 5f3f3974d5347536a098f33eb55826382755b5a8 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 05b4f6a002ef3f090d70b6ade829ca1bf679eac0abe89707ca5ccf3d6d74b193 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: b424ef8f2d9859451976287a408004919705b84b3bc642e1e877560d117acefdd7ea5431438decfcb8e3bc24c5d758156005b869df64c4dfffefa29e9559c60a bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance')], 'duration': 0.001052595000146539, 'start': 1685951452.7712488, 'stop': 1685951452.7723038, '$report_type': 'TestReport', 'item_index': 523, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_hello_workflow + location: ('tests/test_provenance.py', 49, 'test_hello_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + when: runtest + nodeid: tests/test_provenance.py::test_hello_workflow + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_hello_single_tool + location: ('tests/test_provenance.py', 61, 'test_hello_single_tool') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_hello_single_tool', 'location': ('tests/test_provenance.py', 61, 'test_hello_single_tool'), 'keywords': {'test_hello_single_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011711050001395051, 'start': 1685951452.7750342, 'stop': 1685951452.7762072, '$report_type': 'TestReport', 'item_index': 524, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl'")], 'duration': 5.263246608000372, 'start': 1685951447.551656, 'stop': 1685951452.814772, '$report_type': 'TestReport', 'item_index': 484, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl'")], 'duration': 0.0003758709999601706, 'start': 1685951452.815354, 'stop': 1685951452.815731, '$report_type': 'TestReport', 'item_index': 484, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl] + location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_pack_single_tool + location: ('tests/test_pack.py', 67, 'test_pack_single_tool') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_single_tool', 'location': ('tests/test_pack.py', 67, 'test_pack_single_tool'), 'keywords': {'test_pack_single_tool': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00024069299979601055, 'start': 1685951452.816771, 'stop': 1685951452.817013, '$report_type': 'TestReport', 'item_index': 485, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/%E2%98%95%F0%9F%98%8D",\n "basename": "☕ðŸ˜",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmptyp89s5l\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptyp89s5l\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6462540919992534, 'start': 1685951452.424056, 'stop': 1685951453.070296, '$report_type': 'TestReport', 'item_index': 508, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/%E2%98%95%F0%9F%98%8D",\n "basename": "☕ðŸ˜",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmptyp89s5l\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptyp89s5l\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006110310005169595, 'start': 1685951453.071579, 'stop': 1685951453.072191, '$report_type': 'TestReport', 'item_index': 508, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]'), 'keywords': {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015628669998477562, 'start': 1685951453.07393, 'stop': 1685951453.0754938, '$report_type': 'TestReport', 'item_index': 509, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_single_tool', 'location': ('tests/test_pack.py', 67, 'test_pack_single_tool'), 'keywords': {'test_pack_single_tool': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl'")], 'duration': 0.26076059300066845, 'start': 1685951452.8174798, 'stop': 1685951453.078235, '$report_type': 'TestReport', 'item_index': 485, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_single_tool', 'location': ('tests/test_pack.py', 67, 'test_pack_single_tool'), 'keywords': {'test_pack_single_tool': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl'")], 'duration': 0.0001997359995584702, 'start': 1685951453.0787358, 'stop': 1685951453.078937, '$report_type': 'TestReport', 'item_index': 485, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_pack_single_tool + location: ('tests/test_pack.py', 67, 'test_pack_single_tool') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_fragment', 'location': ('tests/test_pack.py', 79, 'test_pack_fragment'), 'keywords': {'test_pack_fragment': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00020665400006691925, 'start': 1685951453.0797708, 'stop': 1685951453.079979, '$report_type': 'TestReport', 'item_index': 486, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_pack_fragment + location: ('tests/test_pack.py', 79, 'test_pack_fragment') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_parallel.py::test_scattered_workflow', 'location': ('tests/test_parallel.py', 23, 'test_scattered_workflow'), 'keywords': {'test_scattered_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] inputs {\n "inp1": [\n "one",\n "two"\n ],\n "inp2": [\n "three",\n "four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] starting step step1_4\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] {\n "echo_in1": "one",\n "echo_in2": "three"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "one"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "three"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_4), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_4] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo$ echo \\\n -n \\\n foo \\\n one \\\n three > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo/step1_out\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] {\n "echo_in1": "two",\n "echo_in2": "four"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "two"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "four"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_5), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_$ echo \\\n -n \\\n foo \\\n two \\\n four > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_/step1_out\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_4] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] outputs {\n "echo_out": "foo one three"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/7k412rnh\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/wm12k6ms\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_5] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] outputs {\n "echo_out": "foo two four"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo one three",\n "foo two four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] outputs {\n "out": [\n "foo one three",\n "foo two four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h4t3gb09\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/302zkbup\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pu7_apaa\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\nDEBUG cwltool:workflow_job.py:777 [workflow _6] inputs {\n "inp1": [\n "one",\n "two"\n ],\n "inp2": [\n "three",\n "four"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _6] starting step step1_4\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:75 [step step1_4] start\nINFO cwltool:workflow_job.py:765 [workflow _6] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_4] {\n "echo_in1": "one",\n "echo_in2": "three"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "one"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "three"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_4), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:job.py:215 [job step1_4] initial work dir {}\nINFO cwltool:job.py:266 [job step1_4] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo$ echo \\\n -n \\\n foo \\\n one \\\n three > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo/step1_out\nDEBUG cwltool:command_line_tool.py:982 [job step1_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:988 [job step1_5] {\n "echo_in1": "two",\n "echo_in2": "four"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "two"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "four"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_5), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job step1_5] initial work dir {}\nINFO cwltool:job.py:266 [job step1_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_$ echo \\\n -n \\\n foo \\\n two \\\n four > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_/step1_out\nINFO cwltool:job.py:419 [job step1_4] completed success\nDEBUG cwltool:job.py:422 [job step1_4] outputs {\n "echo_out": "foo one three"\n}\nDEBUG cwltool:job.py:446 [job step1_4] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/7k412rnh\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:job.py:454 [job step1_4] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/wm12k6ms\nINFO cwltool:job.py:419 [job step1_5] completed success\nDEBUG cwltool:job.py:422 [job step1_5] outputs {\n "echo_out": "foo two four"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo one three",\n "foo two four"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _6] outputs {\n "out": [\n "foo one three",\n "foo two four"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h4t3gb09\nDEBUG cwltool:job.py:454 [job step1_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/302zkbup\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pu7_apaa\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_')], 'duration': 0.8109973410000748, 'start': 1685951452.437483, 'stop': 1685951453.248462, '$report_type': 'TestReport', 'item_index': 495, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_parallel.py::test_scattered_workflow', 'location': ('tests/test_parallel.py', 23, 'test_scattered_workflow'), 'keywords': {'test_scattered_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] inputs {\n "inp1": [\n "one",\n "two"\n ],\n "inp2": [\n "three",\n "four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] starting step step1_4\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] {\n "echo_in1": "one",\n "echo_in2": "three"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "one"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "three"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_4), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_4] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo$ echo \\\n -n \\\n foo \\\n one \\\n three > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo/step1_out\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] {\n "echo_in1": "two",\n "echo_in2": "four"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "two"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "four"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_5), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_$ echo \\\n -n \\\n foo \\\n two \\\n four > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_/step1_out\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_4] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] outputs {\n "echo_out": "foo one three"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/7k412rnh\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/wm12k6ms\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_5] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] outputs {\n "echo_out": "foo two four"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo one three",\n "foo two four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] outputs {\n "out": [\n "foo one three",\n "foo two four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h4t3gb09\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/302zkbup\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pu7_apaa\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\nDEBUG cwltool:workflow_job.py:777 [workflow _6] inputs {\n "inp1": [\n "one",\n "two"\n ],\n "inp2": [\n "three",\n "four"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _6] starting step step1_4\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:75 [step step1_4] start\nINFO cwltool:workflow_job.py:765 [workflow _6] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_4] {\n "echo_in1": "one",\n "echo_in2": "three"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "one"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "three"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_4), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:job.py:215 [job step1_4] initial work dir {}\nINFO cwltool:job.py:266 [job step1_4] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo$ echo \\\n -n \\\n foo \\\n one \\\n three > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo/step1_out\nDEBUG cwltool:command_line_tool.py:982 [job step1_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:988 [job step1_5] {\n "echo_in1": "two",\n "echo_in2": "four"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "two"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "four"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_5), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job step1_5] initial work dir {}\nINFO cwltool:job.py:266 [job step1_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_$ echo \\\n -n \\\n foo \\\n two \\\n four > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_/step1_out\nINFO cwltool:job.py:419 [job step1_4] completed success\nDEBUG cwltool:job.py:422 [job step1_4] outputs {\n "echo_out": "foo one three"\n}\nDEBUG cwltool:job.py:446 [job step1_4] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/7k412rnh\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:job.py:454 [job step1_4] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/wm12k6ms\nINFO cwltool:job.py:419 [job step1_5] completed success\nDEBUG cwltool:job.py:422 [job step1_5] outputs {\n "echo_out": "foo two four"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo one three",\n "foo two four"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _6] outputs {\n "out": [\n "foo one three",\n "foo two four"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h4t3gb09\nDEBUG cwltool:job.py:454 [job step1_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/302zkbup\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pu7_apaa\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_')], 'duration': 0.0004042090004077181, 'start': 1685951453.249595, 'stop': 1685951453.250001, '$report_type': 'TestReport', 'item_index': 495, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_parallel.py::test_scattered_workflow + location: ('tests/test_parallel.py', 23, 'test_scattered_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_spaces_in_input_files + location: ('tests/test_path_checks.py', 39, 'test_spaces_in_input_files') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_spaces_in_input_files', 'location': ('tests/test_path_checks.py', 39, 'test_spaces_in_input_files'), 'keywords': {'test_spaces_in_input_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013412010002866737, 'start': 1685951453.253155, 'stop': 1685951453.254497, '$report_type': 'TestReport', 'item_index': 496, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_require_prefix_workreuse', 'location': ('tests/test_ext.py', 241, 'test_require_prefix_workreuse'), 'keywords': {'test_require_prefix_workreuse': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "page": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt",\n "basename": "time.txt",\n "class": "File",\n "checksum": "sha1$2682bb62398b0d95b2086661579b252fe8c8667c",\n "size": 19,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl'\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] /private/tmp/docker_tmpaadyphdc$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpaadyphdc,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp5uqhdbo1,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpz_91s5q9/20230605095051-050288.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n 'import time\nprint(time.time())\n' > /private/tmp/docker_tmpaadyphdc/time.txt\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/workreuse.cwl:6:1: checking field 'requirements'\ntests/wf/workreuse.cwl:9:3: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#WorkReuse'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/workreuse-fail.cwl:4:1: checking field 'requirements'\ntests/wf/workreuse-fail.cwl:7:3: checking item\n Field 'class' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/WorkReuse'\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job workreuse.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\nDEBUG cwltool:command_line_tool.py:988 [job workreuse.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job workreuse.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job workreuse.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "valueFrom": "import time\\nprint(time.time())\\n",\n "position": [\n 0,\n 1\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job workreuse.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job workreuse.cwl] /private/tmp/docker_tmpaadyphdc$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpaadyphdc,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp5uqhdbo1,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpz_91s5q9/20230605095051-050288.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import time\nprint(time.time())\n\' > /private/tmp/docker_tmpaadyphdc/time.txt\nINFO cwltool:job.py:905 [job workreuse.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job workreuse.cwl] completed success\nDEBUG cwltool:job.py:422 [job workreuse.cwl] outputs {\n "page": {\n "location": "file:///private/tmp/docker_tmpaadyphdc/time.txt",\n "basename": "time.txt",\n "nameroot": "time",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$2682bb62398b0d95b2086661579b252fe8c8667c",\n "size": 19,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job workreuse.cwl] Removing input staging directory /private/tmp/docker_tmpa6x0fmbj\nDEBUG cwltool:job.py:454 [job workreuse.cwl] Removing temporary directory /private/tmp/docker_tmp5uqhdbo1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpaadyphdc/time.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaadyphdc\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/workreuse.cwl:6:1: checking field \'requirements\'\ntests/wf/workreuse.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#WorkReuse\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/workreuse-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/workreuse-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/WorkReuse\'')], 'duration': 3.239526761999514, 'start': 1685951450.218237, 'stop': 1685951453.457684, '$report_type': 'TestReport', 'item_index': 377, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_ext.py::test_require_prefix_workreuse', 'location': ('tests/test_ext.py', 241, 'test_require_prefix_workreuse'), 'keywords': {'test_require_prefix_workreuse': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "page": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt",\n "basename": "time.txt",\n "class": "File",\n "checksum": "sha1$2682bb62398b0d95b2086661579b252fe8c8667c",\n "size": 19,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl'\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] /private/tmp/docker_tmpaadyphdc$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpaadyphdc,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp5uqhdbo1,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpz_91s5q9/20230605095051-050288.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n 'import time\nprint(time.time())\n' > /private/tmp/docker_tmpaadyphdc/time.txt\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/workreuse.cwl:6:1: checking field 'requirements'\ntests/wf/workreuse.cwl:9:3: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#WorkReuse'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/workreuse-fail.cwl:4:1: checking field 'requirements'\ntests/wf/workreuse-fail.cwl:7:3: checking item\n Field 'class' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/WorkReuse'\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job workreuse.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\nDEBUG cwltool:command_line_tool.py:988 [job workreuse.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job workreuse.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job workreuse.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "valueFrom": "import time\\nprint(time.time())\\n",\n "position": [\n 0,\n 1\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job workreuse.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job workreuse.cwl] /private/tmp/docker_tmpaadyphdc$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpaadyphdc,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp5uqhdbo1,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpz_91s5q9/20230605095051-050288.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import time\nprint(time.time())\n\' > /private/tmp/docker_tmpaadyphdc/time.txt\nINFO cwltool:job.py:905 [job workreuse.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job workreuse.cwl] completed success\nDEBUG cwltool:job.py:422 [job workreuse.cwl] outputs {\n "page": {\n "location": "file:///private/tmp/docker_tmpaadyphdc/time.txt",\n "basename": "time.txt",\n "nameroot": "time",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$2682bb62398b0d95b2086661579b252fe8c8667c",\n "size": 19,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job workreuse.cwl] Removing input staging directory /private/tmp/docker_tmpa6x0fmbj\nDEBUG cwltool:job.py:454 [job workreuse.cwl] Removing temporary directory /private/tmp/docker_tmp5uqhdbo1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpaadyphdc/time.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaadyphdc\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/workreuse.cwl:6:1: checking field \'requirements\'\ntests/wf/workreuse.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#WorkReuse\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/workreuse-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/workreuse-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/WorkReuse\'')], 'duration': 0.0004003159992862493, 'start': 1685951453.458577, 'stop': 1685951453.458978, '$report_type': 'TestReport', 'item_index': 377, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_ext.py::test_require_prefix_workreuse + location: ('tests/test_ext.py', 241, 'test_require_prefix_workreuse') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u6e2c\u8a66] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u6e2c\\u8a66]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u6e2c\\u8a66]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u6e2c\\u8a66]'), 'keywords': {'test_unicode_in_input_files[\\u6e2c\\u8a66]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u6e2c\\u8a66': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013005709997742088, 'start': 1685951453.460156, 'stop': 1685951453.461458, '$report_type': 'TestReport', 'item_index': 497, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_hello_single_tool', 'location': ('tests/test_provenance.py', 61, 'test_hello_single_tool'), 'keywords': {'test_hello_single_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl --message Hello tool\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwmeaibo9/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/tmp/docker_tmpjhr7n0cf$ echo \\\n 'Hello tool'\nHello tool\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl --message Hello tool\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\', job_order=[\'--message\', \'Hello tool\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 70dfb26d3325ac63dd94ae620a2af975f669a90e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 533cc58046d17fc0a7016e4c766c10142ecde5fa38aa18dcf974157d580deb4f workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 3bafbb8b5344c26c18de21b65a086a57982365963bf5002ee8d97e34474d2073db852be7d53e773abe848c43fc1f94107d0aa289a681eb180c03a0e2f9ad7b2d workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwmeaibo9/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello tool"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello tool"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello tool"\n }\n]\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/manifest-sha1.txt: a1e591e931fd3bf502a5124e6cdfccee57cf2c8c data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'message\': \'Hello tool\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello tool\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b7bf61dc3c35c1498e63eab30868107dfd3a0e3c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 7b2e41cde05165fb347d46aeb0515678bdb26a3afcdf0be5e1856c7bed8d634d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 37966e8e9fcb932ac3e0f42ff1a18cb5636fa4ac7bcd58efc93db68c746020472f52de406f4b0bd9b52081f61493af76598749efb026bde8e905b993748aeca5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/tmp/docker_tmpjhr7n0cf$ echo \\\n \'Hello tool\'\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/tmp/docker_tmphhy0qgsq\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/tmp/docker_tmp52t5g_kl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjhr7n0cf\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 0df78c0814a11a10649539f01d3f1d27889b6982 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 4fbaed3c12a57f76a1945adfb70b50c87abda26a15bfc13c26d8a64d1ac715fb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 2acf5249b3f87fa61ca22b79412d2e60a73158abe39f4733b637bf8dc36e02f69d656af1542b70b8dff22a955018997f8a61a4b5a56b7372f8c9fa620a17ea6a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b8d0757535ab4b44d791c2d0fbb174ffe0020685 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ce34ee00d40e193df72d84d7184b22595933c0f238f37c1219bf89ac68eba656 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: e267b9020c79e53a71b64343147f6d5162c3a99597d30968ff7fb98ea24129d775422ea7d8be49c4c9506eb8dca960579135e6a6a1a64d772eb64e0b16c51fcc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b4e90a53e0b472130f1c3bb560a913442f3a47ae metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 51af6b9c16424ec42ee90345fdff5ebdfcc2bec9e0bc8d36bdeefe1615b4a55e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: bcc6d25297dbb1fd15fa5c16d6efbe09a7a171aa9ef096706e800d69abd37d790e7ba6b4cf5837969ffeeb36bb52d8c9ad5a01426e35b253e87d7a9367a59c5e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 1f424d204810cc521f65846029233e67a5aecabc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 6712976929fece3a8fd0c89d00625979ba4a55924d6255e0811e72f81c619e2a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: ce2958adaabaea084457006ce34504167cc4b62fed03866acf3ceac0698696db88b8c50caab76154d46981d65fc47993c872d71b8e535158e2f37ca62bc78d83 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: bf91f553672e8e589844171b3eb1a30b09ff30f4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 0ef0ec1f212396cb7142ad4c56de9ca104789b773e15374625c33ca2eea2cadd metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 7dc7bf8259d4ceee588781512469d2e652993e27efa379530596969764d17f1800bdfccb0183d89ba5f3246418bb5ff9ae8e6b8f96299424c4c9f8f5888c32c4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 8bb1519e84453a0303586ecec455a1ab3a1c065b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ce41810d86d8a98ff8dfc2daa5f48418d88001ff2514fe073d4ae6772f5eb569 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: c049305651d388979433c9ae5743b2a028f9f1f8d5911032d924af95fc18c332f78bb69b76445dab3bfecd3da1588372372e9df75c1a612d3a72f633e3866b36 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: bafd8051fd348d6f5a46c638d04450aaec30077f snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 25bfc086e95b92a670c70b9557b42f18f435538008b32350992929a8340affee snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 5e073bc15f1f665f8e28f397c7eac8db6540a5680d19fb87babdfafafe54c01addbc9c0baebc8f5dd9502a441a6fc052378dfbf35773a9cbde2dc16237229c53 snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 9cf58fb7f38279c7e6a34c35961cc01b715dfcea metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 5455ced4b8f23a5656c8433bc0ca86109cbf855efef98c5ff418c3234b7d1b0a metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: e5a1b7a84990feb5fd2f548e6332edbeb1fa1be639757850234bb1dc7ec3c654eb3390ae564f79093caf7aa1a7f10810637f9770e03cdfbfb6d59d82cf4556d4 metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 6645a7d99f8f1cc1da9f4fa5d08397781becbf60 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 41488aa18839c4e43d13985e1798726007163b9257e571cabfdc85603eeb8aaf metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 6af087ee91140194d771105e4fb6d02fca6b69a1305177e56bd9c317f02b8a847eacd7274937809cf0a5f413d60aff0dcce67ac1881519adb865e305122f5a2d metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 86b54373840e653bd1eb0e225ee28d33f12fc74d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: e1c4900574a6d9f1e46ab83d3fc9fde47b51d5ae343aff9302fb99aeb68f6918 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 2476349f33e8a55648fbf251e53a5ca948b6a79deae8cd94df3e744ce8672f42ec24643fb45884e6cfed9a94282e517e0544a5238397d288eb99fdb21b70a5e6 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance')], 'duration': 0.8588609070002349, 'start': 1685951452.77656, 'stop': 1685951453.635401, '$report_type': 'TestReport', 'item_index': 524, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_hello_single_tool', 'location': ('tests/test_provenance.py', 61, 'test_hello_single_tool'), 'keywords': {'test_hello_single_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl --message Hello tool\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwmeaibo9/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/tmp/docker_tmpjhr7n0cf$ echo \\\n 'Hello tool'\nHello tool\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl --message Hello tool\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\', job_order=[\'--message\', \'Hello tool\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 70dfb26d3325ac63dd94ae620a2af975f669a90e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 533cc58046d17fc0a7016e4c766c10142ecde5fa38aa18dcf974157d580deb4f workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 3bafbb8b5344c26c18de21b65a086a57982365963bf5002ee8d97e34474d2073db852be7d53e773abe848c43fc1f94107d0aa289a681eb180c03a0e2f9ad7b2d workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwmeaibo9/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello tool"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello tool"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello tool"\n }\n]\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/manifest-sha1.txt: a1e591e931fd3bf502a5124e6cdfccee57cf2c8c data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'message\': \'Hello tool\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello tool\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b7bf61dc3c35c1498e63eab30868107dfd3a0e3c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 7b2e41cde05165fb347d46aeb0515678bdb26a3afcdf0be5e1856c7bed8d634d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 37966e8e9fcb932ac3e0f42ff1a18cb5636fa4ac7bcd58efc93db68c746020472f52de406f4b0bd9b52081f61493af76598749efb026bde8e905b993748aeca5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/tmp/docker_tmpjhr7n0cf$ echo \\\n \'Hello tool\'\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/tmp/docker_tmphhy0qgsq\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/tmp/docker_tmp52t5g_kl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjhr7n0cf\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 0df78c0814a11a10649539f01d3f1d27889b6982 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 4fbaed3c12a57f76a1945adfb70b50c87abda26a15bfc13c26d8a64d1ac715fb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 2acf5249b3f87fa61ca22b79412d2e60a73158abe39f4733b637bf8dc36e02f69d656af1542b70b8dff22a955018997f8a61a4b5a56b7372f8c9fa620a17ea6a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b8d0757535ab4b44d791c2d0fbb174ffe0020685 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ce34ee00d40e193df72d84d7184b22595933c0f238f37c1219bf89ac68eba656 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: e267b9020c79e53a71b64343147f6d5162c3a99597d30968ff7fb98ea24129d775422ea7d8be49c4c9506eb8dca960579135e6a6a1a64d772eb64e0b16c51fcc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b4e90a53e0b472130f1c3bb560a913442f3a47ae metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 51af6b9c16424ec42ee90345fdff5ebdfcc2bec9e0bc8d36bdeefe1615b4a55e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: bcc6d25297dbb1fd15fa5c16d6efbe09a7a171aa9ef096706e800d69abd37d790e7ba6b4cf5837969ffeeb36bb52d8c9ad5a01426e35b253e87d7a9367a59c5e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 1f424d204810cc521f65846029233e67a5aecabc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 6712976929fece3a8fd0c89d00625979ba4a55924d6255e0811e72f81c619e2a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: ce2958adaabaea084457006ce34504167cc4b62fed03866acf3ceac0698696db88b8c50caab76154d46981d65fc47993c872d71b8e535158e2f37ca62bc78d83 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: bf91f553672e8e589844171b3eb1a30b09ff30f4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 0ef0ec1f212396cb7142ad4c56de9ca104789b773e15374625c33ca2eea2cadd metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 7dc7bf8259d4ceee588781512469d2e652993e27efa379530596969764d17f1800bdfccb0183d89ba5f3246418bb5ff9ae8e6b8f96299424c4c9f8f5888c32c4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 8bb1519e84453a0303586ecec455a1ab3a1c065b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ce41810d86d8a98ff8dfc2daa5f48418d88001ff2514fe073d4ae6772f5eb569 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: c049305651d388979433c9ae5743b2a028f9f1f8d5911032d924af95fc18c332f78bb69b76445dab3bfecd3da1588372372e9df75c1a612d3a72f633e3866b36 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: bafd8051fd348d6f5a46c638d04450aaec30077f snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 25bfc086e95b92a670c70b9557b42f18f435538008b32350992929a8340affee snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 5e073bc15f1f665f8e28f397c7eac8db6540a5680d19fb87babdfafafe54c01addbc9c0baebc8f5dd9502a441a6fc052378dfbf35773a9cbde2dc16237229c53 snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 9cf58fb7f38279c7e6a34c35961cc01b715dfcea metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 5455ced4b8f23a5656c8433bc0ca86109cbf855efef98c5ff418c3234b7d1b0a metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: e5a1b7a84990feb5fd2f548e6332edbeb1fa1be639757850234bb1dc7ec3c654eb3390ae564f79093caf7aa1a7f10810637f9770e03cdfbfb6d59d82cf4556d4 metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 6645a7d99f8f1cc1da9f4fa5d08397781becbf60 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 41488aa18839c4e43d13985e1798726007163b9257e571cabfdc85603eeb8aaf metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 6af087ee91140194d771105e4fb6d02fca6b69a1305177e56bd9c317f02b8a847eacd7274937809cf0a5f413d60aff0dcce67ac1881519adb865e305122f5a2d metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 86b54373840e653bd1eb0e225ee28d33f12fc74d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: e1c4900574a6d9f1e46ab83d3fc9fde47b51d5ae343aff9302fb99aeb68f6918 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 2476349f33e8a55648fbf251e53a5ca948b6a79deae8cd94df3e744ce8672f42ec24643fb45884e6cfed9a94282e517e0544a5238397d288eb99fdb21b70a5e6 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance')], 'duration': 0.0006209440007296507, 'start': 1685951453.636877, 'stop': 1685951453.6374998, '$report_type': 'TestReport', 'item_index': 524, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_hello_single_tool + location: ('tests/test_provenance.py', 61, 'test_hello_single_tool') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + when: runtest + nodeid: tests/test_provenance.py::test_hello_single_tool + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_revsort_workflow + location: ('tests/test_provenance.py', 74, 'test_revsort_workflow') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow', 'location': ('tests/test_provenance.py', 74, 'test_revsort_workflow'), 'keywords': {'test_revsort_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011466310006653657, 'start': 1685951453.639364, 'stop': 1685951453.640511, '$report_type': 'TestReport', 'item_index': 525, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]'), 'keywords': {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "امتحان",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpu7fd0k2e\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu7fd0k2e\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6586480109999684, 'start': 1685951453.075871, 'stop': 1685951453.734503, '$report_type': 'TestReport', 'item_index': 509, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]'), 'keywords': {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "امتحان",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpu7fd0k2e\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu7fd0k2e\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005586230008702842, 'start': 1685951453.7356002, 'stop': 1685951453.736159, '$report_type': 'TestReport', 'item_index': 509, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013699379996978678, 'start': 1685951453.7374332, 'stop': 1685951453.7388039, '$report_type': 'TestReport', 'item_index': 510, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_fragment', 'location': ('tests/test_pack.py', 79, 'test_pack_fragment'), 'keywords': {'test_pack_fragment': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl'\nURI prefix 'keep' of 'keep:99999999999999999999999999999999+118/token.txt' not recognized, are you missing a $namespaces section?\ntests/wf/scatter2.cwl:18:7: Warning: Unsupported scheme 'keep' in url:\n keep:99999999999999999999999999999999+118/token.txt\ntests/wf/scatter2.cwl:36:9: Warning: checking item\n Warning: Field 'class' contains undefined reference to\n 'http://arvados.org/cwl#RunInSingleContainer'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'keep' of 'keep:99999999999999999999999999999999+118/token.txt' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1157 tests/wf/scatter2.cwl:18:7: Warning: Unsupported scheme 'keep' in url:\n keep:99999999999999999999999999999999+118/token.txt\nWARNING salad:ref_resolver.py:1157 tests/wf/scatter2.cwl:36:9: Warning: checking item\n Warning: Field 'class' contains undefined reference to\n 'http://arvados.org/cwl#RunInSingleContainer'")], 'duration': 0.7120275979996222, 'start': 1685951453.0802948, 'stop': 1685951453.792306, '$report_type': 'TestReport', 'item_index': 486, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_fragment', 'location': ('tests/test_pack.py', 79, 'test_pack_fragment'), 'keywords': {'test_pack_fragment': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl'\nURI prefix 'keep' of 'keep:99999999999999999999999999999999+118/token.txt' not recognized, are you missing a $namespaces section?\ntests/wf/scatter2.cwl:18:7: Warning: Unsupported scheme 'keep' in url:\n keep:99999999999999999999999999999999+118/token.txt\ntests/wf/scatter2.cwl:36:9: Warning: checking item\n Warning: Field 'class' contains undefined reference to\n 'http://arvados.org/cwl#RunInSingleContainer'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'keep' of 'keep:99999999999999999999999999999999+118/token.txt' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1157 tests/wf/scatter2.cwl:18:7: Warning: Unsupported scheme 'keep' in url:\n keep:99999999999999999999999999999999+118/token.txt\nWARNING salad:ref_resolver.py:1157 tests/wf/scatter2.cwl:36:9: Warning: checking item\n Warning: Field 'class' contains undefined reference to\n 'http://arvados.org/cwl#RunInSingleContainer'")], 'duration': 0.00022919200000615092, 'start': 1685951453.792846, 'stop': 1685951453.793076, '$report_type': 'TestReport', 'item_index': 486, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_pack_fragment + location: ('tests/test_pack.py', 79, 'test_pack_fragment') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_rewrites', 'location': ('tests/test_pack.py', 96, 'test_pack_rewrites'), 'keywords': {'test_pack_rewrites': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00026976899971487, 'start': 1685951453.794219, 'stop': 1685951453.79449, '$report_type': 'TestReport', 'item_index': 487, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_pack_rewrites + location: ('tests/test_pack.py', 96, 'test_pack_rewrites') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_rewrites', 'location': ('tests/test_pack.py', 96, 'test_pack_rewrites'), 'keywords': {'test_pack_rewrites': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default-wf5.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default-wf5.cwl'\ntests/wf/default-dir5.cwl:20:13: Warning: Field 'location' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/inp1'\ntests/wf/default-dir5.cwl:20:13: Warning: Field 'location' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/inp1'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default-wf5.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default-wf5.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/default-dir5.cwl:20:13: Warning: Field 'location' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/inp1'\nWARNING salad:ref_resolver.py:1157 tests/wf/default-dir5.cwl:20:13: Warning: Field 'location' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/inp1'")], 'duration': 0.05521076900004118, 'start': 1685951453.7949681, 'stop': 1685951453.8501801, '$report_type': 'TestReport', 'item_index': 487, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_rewrites', 'location': ('tests/test_pack.py', 96, 'test_pack_rewrites'), 'keywords': {'test_pack_rewrites': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default-wf5.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default-wf5.cwl'\ntests/wf/default-dir5.cwl:20:13: Warning: Field 'location' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/inp1'\ntests/wf/default-dir5.cwl:20:13: Warning: Field 'location' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/inp1'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default-wf5.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default-wf5.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/default-dir5.cwl:20:13: Warning: Field 'location' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/inp1'\nWARNING salad:ref_resolver.py:1157 tests/wf/default-dir5.cwl:20:13: Warning: Field 'location' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/inp1'")], 'duration': 0.0003576639992388664, 'start': 1685951453.851042, 'stop': 1685951453.8514009, '$report_type': 'TestReport', 'item_index': 487, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_pack_rewrites + location: ('tests/test_pack.py', 96, 'test_pack_rewrites') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl] + location: ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl]', 'location': ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl]'), 'keywords': {'test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/hello_single_tool.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005587510004261276, 'start': 1685951453.853943, 'stop': 1685951453.854503, '$report_type': 'TestReport', 'item_index': 488, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl]', 'location': ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl]'), 'keywords': {'test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/hello_single_tool.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'")], 'duration': 0.021784423999633873, 'start': 1685951453.8550668, 'stop': 1685951453.876853, '$report_type': 'TestReport', 'item_index': 488, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl]', 'location': ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl]'), 'keywords': {'test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/hello_single_tool.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'")], 'duration': 0.000250588000199059, 'start': 1685951453.877302, 'stop': 1685951453.877553, '$report_type': 'TestReport', 'item_index': 488, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl] + location: ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello_single_tool.cwl]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_relocate.py::test_relocate_symlinks + location: ('tests/test_relocate.py', 57, 'test_relocate_symlinks') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_relocate_symlinks', 'location': ('tests/test_relocate.py', 57, 'test_relocate_symlinks'), 'keywords': {'test_relocate_symlinks': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011758240007111453, 'start': 1685951453.878428, 'stop': 1685951453.8796039, '$report_type': 'TestReport', 'item_index': 577, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u6e2c\\u8a66]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u6e2c\\u8a66]'), 'keywords': {'test_unicode_in_input_files[\\u6e2c\\u8a66]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u6e2c\\u8a66': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": 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\'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66",\n "size": 0,\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66",\n "/private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201/\\u6e2c\\u8a66",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": 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\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script",\n "input": {\n "class": "File",\n "location": 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[\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66",\n "/private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201/\\u6e2c\\u8a66",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66",\n "size": 0,\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": "",\n "path": "/private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201/\\u6e2c\\u8a66",\n "dirname": "/private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script] initial work dir {}\nINFO cwltool:job.py:266 [job script] /private/tmp/docker_tmpfc21sv3y$ cat \\\n /private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201/測試 > /private/tmp/docker_tmpfc21sv3y/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script] completed success\nDEBUG cwltool:job.py:422 [job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpfc21sv3y/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script] Removing input staging directory /private/tmp/docker_tmpq3rcg_oj\nDEBUG cwltool:job.py:454 [job script] Removing temporary directory /private/tmp/docker_tmpsvv2n4_3\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpfc21sv3y/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfc21sv3y\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6394740679997994, 'start': 1685951453.461801, 'stop': 1685951454.1012611, '$report_type': 'TestReport', 'item_index': 497, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u6e2c\\u8a66]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u6e2c\\u8a66]'), 'keywords': {'test_unicode_in_input_files[\\u6e2c\\u8a66]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u6e2c\\u8a66': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script",\n "input": {\n "class": "File",\n "location": 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"/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66",\n "/private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201/\\u6e2c\\u8a66",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66",\n "size": 0,\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": "",\n "path": "/private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201/\\u6e2c\\u8a66",\n "dirname": "/private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] /private/tmp/docker_tmpfc21sv3y$ cat \\\n /private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201/測試 > /private/tmp/docker_tmpfc21sv3y/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpfc21sv3y/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing input staging directory /private/tmp/docker_tmpq3rcg_oj\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing temporary directory /private/tmp/docker_tmpsvv2n4_3\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpfc21sv3y/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpfc21sv3y\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/script\nDEBUG cwltool:command_line_tool.py:988 [job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66",\n "size": 0,\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66",\n "/private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201/\\u6e2c\\u8a66",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/\\u6e2c\\u8a66",\n "size": 0,\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": "",\n "path": "/private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201/\\u6e2c\\u8a66",\n "dirname": "/private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script] initial work dir {}\nINFO cwltool:job.py:266 [job script] /private/tmp/docker_tmpfc21sv3y$ cat \\\n /private/tmp/docker_tmpq3rcg_oj/stg48f59e7d-18d0-4195-bc5e-e9c43fa2c201/測試 > /private/tmp/docker_tmpfc21sv3y/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script] completed success\nDEBUG cwltool:job.py:422 [job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpfc21sv3y/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script] Removing input staging directory /private/tmp/docker_tmpq3rcg_oj\nDEBUG cwltool:job.py:454 [job script] Removing temporary directory /private/tmp/docker_tmpsvv2n4_3\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpfc21sv3y/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfc21sv3y\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005973909992462723, 'start': 1685951454.102369, 'stop': 1685951454.102967, '$report_type': 'TestReport', 'item_index': 497, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u6e2c\u8a66] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u6e2c\\u8a66]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\uadf8\ub798\ud504] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\uadf8\\ub798\\ud504]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]'), 'keywords': {'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0020320819994594785, 'start': 1685951454.104286, 'stop': 1685951454.10632, '$report_type': 'TestReport', 'item_index': 498, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj2n4e2tf\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj2n4e2tf\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6722589929995593, 'start': 1685951453.739232, 'stop': 1685951454.411476, '$report_type': 'TestReport', 'item_index': 510, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj2n4e2tf\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj2n4e2tf\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0010611549996610847, 'start': 1685951454.412545, 'stop': 1685951454.4136078, '$report_type': 'TestReport', 'item_index': 510, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names + location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_clt_returns_specialchar_names', 'location': ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names'), 'keywords': {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001187488999676134, 'start': 1685951454.415158, 'stop': 1685951454.416346, '$report_type': 'TestReport', 'item_index': 511, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_clt_returns_specialchar_names', 'location': ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names'), 'keywords': {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0065578280000408995, 'start': 1685951454.416679, 'stop': 1685951454.4232378, '$report_type': 'TestReport', 'item_index': 511, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_clt_returns_specialchar_names', 'location': ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names'), 'keywords': {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002504579997548717, 'start': 1685951454.423627, 'stop': 1685951454.423879, '$report_type': 'TestReport', 'item_index': 511, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names + location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_pathmapper.py::test_subclass + location: ('tests/test_pathmapper.py', 8, 'test_subclass') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_subclass', 'location': ('tests/test_pathmapper.py', 8, 'test_subclass'), 'keywords': {'test_subclass': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00020675299947470194, 'start': 1685951454.4253829, 'stop': 1685951454.425591, '$report_type': 'TestReport', 'item_index': 512, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_subclass', 'location': ('tests/test_pathmapper.py', 8, 'test_subclass'), 'keywords': {'test_subclass': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00025883699981932295, 'start': 1685951454.4258912, 'stop': 1685951454.4261508, '$report_type': 'TestReport', 'item_index': 512, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_pathmapper.py::test_subclass', 'location': ('tests/test_pathmapper.py', 8, 'test_subclass'), 'keywords': {'test_subclass': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00017651699999987613, 'start': 1685951454.426451, 'stop': 1685951454.426628, '$report_type': 'TestReport', 'item_index': 512, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_pathmapper.py::test_subclass + location: ('tests/test_pathmapper.py', 8, 'test_subclass') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_secrets.py::test_secrets[-expected1] + location: ('tests/test_secrets.py', 40, 'test_secrets[-expected1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected1]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected1]'), 'keywords': {'test_secrets[-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected1': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007169380005507264, 'start': 1685951454.427757, 'stop': 1685951454.4284759, '$report_type': 'TestReport', 'item_index': 581, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> -expected1]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -expected1]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: -expected1]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected1]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected1]'), 'keywords': {'test_secrets[-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected1': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000249826000072062, 'start': 1685951454.42887, 'stop': 1685951454.429121, '$report_type': 'TestReport', 'item_index': 581, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> -expected1]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -expected1]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: -expected1]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected1]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected1]'), 'keywords': {'test_secrets[-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected1': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002683279999473598, 'start': 1685951454.429458, 'stop': 1685951454.429728, '$report_type': 'TestReport', 'item_index': 581, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> -expected1]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -expected1]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: -expected1]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_secrets.py::test_secrets[-expected1] + location: ('tests/test_secrets.py', 40, 'test_secrets[-expected1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_secrets.py::test_secrets[-expected2] + location: ('tests/test_secrets.py', 40, 'test_secrets[-expected2]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected2]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected2]'), 'keywords': {'test_secrets[-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected2': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006197129996508011, 'start': 1685951454.4304729, 'stop': 1685951454.431094, '$report_type': 'TestReport', 'item_index': 582, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> -expected2]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -expected2]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: -expected2]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected2]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected2]'), 'keywords': {'test_secrets[-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected2': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003470820001894026, 'start': 1685951454.431703, 'stop': 1685951454.432051, '$report_type': 'TestReport', 'item_index': 582, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> -expected2]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -expected2]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: -expected2]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected2]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected2]'), 'keywords': {'test_secrets[-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected2': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004827409993595211, 'start': 1685951454.432508, 'stop': 1685951454.432993, '$report_type': 'TestReport', 'item_index': 582, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> -expected2]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -expected2]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: -expected2]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_secrets.py::test_secrets[-expected2] + location: ('tests/test_secrets.py', 40, 'test_secrets[-expected2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_secrets.py::test_secret_workflow_log + location: ('tests/test_secrets.py', 59, 'test_secret_workflow_log') + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log', 'location': ('tests/test_secrets.py', 59, 'test_secret_workflow_log'), 'keywords': {'test_secret_workflow_log': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00021649700011039386, 'start': 1685951454.433845, 'stop': 1685951454.434062, '$report_type': 'TestReport', 'item_index': 583, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_spaces_in_input_files', 'location': ('tests/test_path_checks.py', 39, 'test_spaces_in_input_files'), 'keywords': {'test_spaces_in_input_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error:\nInvalid filename: \'test with spaces\' contains illegal characters\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1315, in main\n (out, status) = real_executor(\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 61, in __call__\n return self.execute(process, job_order_object, runtime_context, logger)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 144, in execute\n self.run_jobs(process, job_order_object, logger, runtime_context)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 217, in run_jobs\n for job in jobiter:\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 995, in job\n visit_class([builder.files, builder.bindings], ("File", "Directory"), _check_adjust)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 379, in check_adjust\n raise WorkflowException(\ncwltool.errors.WorkflowException: Invalid filename: \'test with spaces\' contains illegal characters\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": "",\n "path": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "dirname": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmpjob2jn5j$ cat \\\n \'/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces\' > /private/tmp/docker_tmpjob2jn5j/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjob2jn5j/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmp0vvpiege\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp6fg7354d\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjob2jn5j/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjob2jn5j\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\nDEBUG cwltool:command_line_tool.py:988 [job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\nERROR cwltool:main.py:1380 Workflow error:\nInvalid filename: \'test with spaces\' contains illegal characters\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1315, in main\n (out, status) = real_executor(\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 61, in __call__\n return self.execute(process, job_order_object, runtime_context, logger)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 144, in execute\n self.run_jobs(process, job_order_object, logger, runtime_context)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 217, in run_jobs\n for job in jobiter:\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 995, in job\n visit_class([builder.files, builder.bindings], ("File", "Directory"), _check_adjust)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 379, in check_adjust\n raise WorkflowException(\ncwltool.errors.WorkflowException: Invalid filename: \'test with spaces\' contains illegal characters\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": "",\n "path": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "dirname": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmpjob2jn5j$ cat \\\n \'/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces\' > /private/tmp/docker_tmpjob2jn5j/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjob2jn5j/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmp0vvpiege\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp6fg7354d\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjob2jn5j/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjob2jn5j\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.3361983879995023, 'start': 1685951453.254849, 'stop': 1685951454.591017, '$report_type': 'TestReport', 'item_index': 496, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_spaces_in_input_files', 'location': ('tests/test_path_checks.py', 39, 'test_spaces_in_input_files'), 'keywords': {'test_spaces_in_input_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error:\nInvalid filename: \'test with spaces\' contains illegal characters\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1315, in main\n (out, status) = real_executor(\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 61, in __call__\n return self.execute(process, job_order_object, runtime_context, logger)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 144, in execute\n self.run_jobs(process, job_order_object, logger, runtime_context)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 217, in run_jobs\n for job in jobiter:\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 995, in job\n visit_class([builder.files, builder.bindings], ("File", "Directory"), _check_adjust)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 379, in check_adjust\n raise WorkflowException(\ncwltool.errors.WorkflowException: Invalid filename: \'test with spaces\' contains illegal characters\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": "",\n "path": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "dirname": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmpjob2jn5j$ cat \\\n \'/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces\' > /private/tmp/docker_tmpjob2jn5j/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjob2jn5j/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmp0vvpiege\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp6fg7354d\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjob2jn5j/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjob2jn5j\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\nDEBUG cwltool:command_line_tool.py:988 [job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\nERROR cwltool:main.py:1380 Workflow error:\nInvalid filename: \'test with spaces\' contains illegal characters\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1315, in main\n (out, status) = real_executor(\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 61, in __call__\n return self.execute(process, job_order_object, runtime_context, logger)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 144, in execute\n self.run_jobs(process, job_order_object, logger, runtime_context)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 217, in run_jobs\n for job in jobiter:\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 995, in job\n visit_class([builder.files, builder.bindings], ("File", "Directory"), _check_adjust)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 379, in check_adjust\n raise WorkflowException(\ncwltool.errors.WorkflowException: Invalid filename: \'test with spaces\' contains illegal characters\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": "",\n "path": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "dirname": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmpjob2jn5j$ cat \\\n \'/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces\' > /private/tmp/docker_tmpjob2jn5j/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjob2jn5j/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmp0vvpiege\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp6fg7354d\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjob2jn5j/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjob2jn5j\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.001422736000677105, 'start': 1685951454.592406, 'stop': 1685951454.5938299, '$report_type': 'TestReport', 'item_index': 496, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_spaces_in_input_files + location: ('tests/test_path_checks.py', 39, 'test_spaces_in_input_files') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_recursive_validation.py::test_recursive_validation + location: ('tests/test_recursive_validation.py', 6, 'test_recursive_validation') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_recursive_validation.py::test_recursive_validation', 'location': ('tests/test_recursive_validation.py', 6, 'test_recursive_validation'), 'keywords': {'test_recursive_validation': 1, 'test_recursive_validation.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00027750600020226557, 'start': 1685951454.5955992, 'stop': 1685951454.595878, '$report_type': 'TestReport', 'item_index': 573, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_recursive_validation.py::test_recursive_validation', 'location': ('tests/test_recursive_validation.py', 6, 'test_recursive_validation'), 'keywords': {'test_recursive_validation': 1, 'test_recursive_validation.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:54]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl'\ntests/wf/default_path.cwl:9:7: Warning: Field 'path' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default.txt'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/default_path.cwl:9:7: Warning: Field 'path' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default.txt'")], 'duration': 0.017540503999953216, 'start': 1685951454.59646, 'stop': 1685951454.614002, '$report_type': 'TestReport', 'item_index': 573, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_recursive_validation.py::test_recursive_validation', 'location': ('tests/test_recursive_validation.py', 6, 'test_recursive_validation'), 'keywords': {'test_recursive_validation': 1, 'test_recursive_validation.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:54]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl'\ntests/wf/default_path.cwl:9:7: Warning: Field 'path' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default.txt'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/default_path.cwl:9:7: Warning: Field 'path' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default.txt'")], 'duration': 0.00020327099991845898, 'start': 1685951454.614452, 'stop': 1685951454.614657, '$report_type': 'TestReport', 'item_index': 573, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_recursive_validation.py::test_recursive_validation + location: ('tests/test_recursive_validation.py', 6, 'test_recursive_validation') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_relocate.py::test_for_910 + location: ('tests/test_relocate.py', 14, 'test_for_910') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_for_910', 'location': ('tests/test_relocate.py', 14, 'test_for_910'), 'keywords': {'test_for_910': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011727219998647342, 'start': 1685951454.615575, 'stop': 1685951454.61675, '$report_type': 'TestReport', 'item_index': 574, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_relocate_symlinks', 'location': ('tests/test_relocate.py', 57, 'test_relocate_symlinks'), 'keywords': {'test_relocate_symlinks': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "bar": {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo",\n "basename": "foo",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\ntotal 0\nlrwxr-xr-x 1 jasperk wheel 46 Jun 5 09:50 dir2 -> /Users/jasperk/gitlab/cwltool/tests/reloc/dir2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmphfn_s4u0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\nDEBUG cwltool:command_line_tool.py:988 [job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job test.cwl] completed success\nDEBUG cwltool:job.py:422 [job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\nDEBUG cwltool:job.py:454 [job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmphfn_s4u0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7850257770005555, 'start': 1685951453.879943, 'stop': 1685951454.664951, '$report_type': 'TestReport', 'item_index': 577, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_relocate_symlinks', 'location': ('tests/test_relocate.py', 57, 'test_relocate_symlinks'), 'keywords': {'test_relocate_symlinks': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "bar": {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo",\n "basename": "foo",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\ntotal 0\nlrwxr-xr-x 1 jasperk wheel 46 Jun 5 09:50 dir2 -> /Users/jasperk/gitlab/cwltool/tests/reloc/dir2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmphfn_s4u0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\nDEBUG cwltool:command_line_tool.py:988 [job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job test.cwl] completed success\nDEBUG cwltool:job.py:422 [job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\nDEBUG cwltool:job.py:454 [job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmphfn_s4u0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007529229997089715, 'start': 1685951454.666344, 'stop': 1685951454.667098, '$report_type': 'TestReport', 'item_index': 577, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_relocate.py::test_relocate_symlinks + location: ('tests/test_relocate.py', 57, 'test_relocate_symlinks') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_schemadef.py::test_schemadef + location: ('tests/test_schemadef.py', 7, 'test_schemadef') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_schemadef.py::test_schemadef', 'location': ('tests/test_schemadef.py', 7, 'test_schemadef'), 'keywords': {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00033530900054756785, 'start': 1685951454.669056, 'stop': 1685951454.6693928, '$report_type': 'TestReport', 'item_index': 578, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\uadf8\\ub798\\ud504]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]'), 'keywords': {'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "path": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "dirname": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmpcqcthnlx$ cat \\\n /private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/그래프 > /private/tmp/docker_tmpcqcthnlx/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpcqcthnlx/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmpmcy_zp2s\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmpfyrojqm7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpcqcthnlx/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpcqcthnlx\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "path": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "dirname": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmpcqcthnlx$ cat \\\n /private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/그래프 > /private/tmp/docker_tmpcqcthnlx/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpcqcthnlx/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpmcy_zp2s\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmpfyrojqm7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpcqcthnlx/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcqcthnlx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7386569559994314, 'start': 1685951454.106852, 'stop': 1685951454.845493, '$report_type': 'TestReport', 'item_index': 498, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\uadf8\\ub798\\ud504]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]'), 'keywords': {'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "path": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "dirname": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmpcqcthnlx$ cat \\\n /private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/그래프 > /private/tmp/docker_tmpcqcthnlx/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpcqcthnlx/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmpmcy_zp2s\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmpfyrojqm7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpcqcthnlx/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpcqcthnlx\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "path": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "dirname": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmpcqcthnlx$ cat \\\n /private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/그래프 > /private/tmp/docker_tmpcqcthnlx/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpcqcthnlx/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpmcy_zp2s\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmpfyrojqm7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpcqcthnlx/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcqcthnlx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006455060001826496, 'start': 1685951454.846982, 'stop': 1685951454.847629, '$report_type': 'TestReport', 'item_index': 498, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\uadf8\ub798\ud504] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u0433\u0440\u0430\u0444\u0438\u043a] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]'), 'keywords': {'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0025021310002557584, 'start': 1685951454.8497221, 'stop': 1685951454.852226, '$report_type': 'TestReport', 'item_index': 499, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]'), 'keywords': {'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "path": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "dirname": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmpvbrqfcce$ cat \\\n /private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/график > /private/tmp/docker_tmpvbrqfcce/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvbrqfcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmps8z5vcf7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmpmxdb7u8w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpvbrqfcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvbrqfcce\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "path": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "dirname": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmpvbrqfcce$ cat \\\n /private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/график > /private/tmp/docker_tmpvbrqfcce/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvbrqfcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmps8z5vcf7\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmpmxdb7u8w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvbrqfcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvbrqfcce\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6572173209997345, 'start': 1685951454.852916, 'stop': 1685951455.510119, '$report_type': 'TestReport', 'item_index': 499, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]'), 'keywords': {'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "path": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "dirname": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmpvbrqfcce$ cat \\\n /private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/график > /private/tmp/docker_tmpvbrqfcce/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvbrqfcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmps8z5vcf7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmpmxdb7u8w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpvbrqfcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvbrqfcce\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "path": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "dirname": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmpvbrqfcce$ cat \\\n /private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/график > /private/tmp/docker_tmpvbrqfcce/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvbrqfcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmps8z5vcf7\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmpmxdb7u8w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvbrqfcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvbrqfcce\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005697329997929046, 'start': 1685951455.511276, 'stop': 1685951455.511847, '$report_type': 'TestReport', 'item_index': 499, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u0433\u0440\u0430\u0444\u0438\u043a] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\U00012043] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\U00012043]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\U00012043]'), 'keywords': {'test_unicode_in_input_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001521131000117748, 'start': 1685951455.513267, 'stop': 1685951455.514789, '$report_type': 'TestReport', 'item_index': 500, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\U00012043]'), 'keywords': {'test_unicode_in_input_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "path": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "dirname": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmp3zambcce$ cat \\\n /private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/ð’ƒ > /private/tmp/docker_tmp3zambcce/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp3zambcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmp2gyrl7es\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmplnp87_ml\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp3zambcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp3zambcce\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "path": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "dirname": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmp3zambcce$ cat \\\n /private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/ð’ƒ > /private/tmp/docker_tmp3zambcce/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp3zambcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmp2gyrl7es\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmplnp87_ml\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp3zambcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3zambcce\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6731989129993963, 'start': 1685951455.515143, 'stop': 1685951456.188326, '$report_type': 'TestReport', 'item_index': 500, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\U00012043]'), 'keywords': {'test_unicode_in_input_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "path": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "dirname": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmp3zambcce$ cat \\\n /private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/ð’ƒ > /private/tmp/docker_tmp3zambcce/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp3zambcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmp2gyrl7es\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmplnp87_ml\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp3zambcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp3zambcce\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "path": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "dirname": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmp3zambcce$ cat \\\n /private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/ð’ƒ > /private/tmp/docker_tmp3zambcce/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp3zambcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmp2gyrl7es\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmplnp87_ml\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp3zambcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3zambcce\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005871860003026086, 'start': 1685951456.189573, 'stop': 1685951456.190162, '$report_type': 'TestReport', 'item_index': 500, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\U00012043] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\U00012043]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u2615\U0001f60d] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u2615\\U0001f60d]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_input_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015364820001195767, 'start': 1685951456.1915379, 'stop': 1685951456.193076, '$report_type': 'TestReport', 'item_index': 501, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow', 'location': ('tests/test_provenance.py', 169, 'test_directory_workflow'), 'keywords': {'test_directory_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "dir1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1"\n },\n "listing": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0\ntest_directory_workflow0/\n cwltool-run/\n 9da56764e3939493b1b27e23e1a15413ad3c7789\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir2/\n a\n c\n b\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3ca69e8d6c234a469d16ac28a4a658c92267c423\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n metadata/\n directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n manifest.json\n directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n logs/\n engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp9k6tej38/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\n\x1b[1;30mINFO\x1b[0m [workflow _18] start\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmpkt9xn476$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpkt9xn476,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp5bdr87x6,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpijlt4w41/20230605095053-735575.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/ZYBRaV\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpu2ojz1u2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpu2ojz1u2,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1tlylhil,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2,target=/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2,readonly \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpl041cwt9/20230605095054-807591.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2 > /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 042ddf8c8e3a821bd2b1e0b31a7e999d8b6358cf workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 24bbc4fbeba486e56a28be585526c2bfea369513cfd06abeeae6f38289755031 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: adc92e3ab02558f989f144b96d6ff9faf8db91d319f1611c703cb2aaf05062ff6c88fa7376128236b98ba553c2f4e51d88a9cf878fb25a435b907b96318c87f5 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp9k6tej38/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\', \'basename\': \'dir2\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\', \'basename\': \'dir2\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e2a2c4c0c09ac506044b76ffa3081669e50a8ff3 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: d8a50ec3ed7c9940992d5d94ad6f81fe7939d212e7e4267d8999537ea4c1f646 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 3b93050d00a41067c2b8308f1513c3f4c66f1d61d0255c926adb5a4676e5a4174c1764345be25ec811c6c9011799d8427b5f2a9865ee167e4cdd4dd6a30d24f8 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 65d233a8c5869bfb70c5a96f3ccca98fc755c3cd metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 9e0308c4e8c8b0510143d7bc960cfbc97d913a436f42304fb901bf90703192af metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 2ab14b39b928bae6b37bc1b9768a16e683c7b90f7ba46f7fe8c137e1264de2a40e06bfa24120beb97dab2b6fa013ac518d12fcda42bb0f950b8bdf052c1f7107 metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#generate/23607ac8-6d07-4c00-9c5b-47c558e7e9e3 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmpkt9xn476$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpkt9xn476,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp5bdr87x6,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpijlt4w41/20230605095053-735575.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 198893dacc70f008f36bbba2fe29d8535c5bd23c metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 120d87f124da54fd9a263778a81bda3cf1a045665303d8422d7d027a264a647d metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: cf443274e5daf84d8ac240b69e536f9a8017420be7388845de2a8a12a3b31e0500a5e17aae827602fa5214ebb387d8dc1f334530a1fff49734bedeb9185376eb metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 1c8ccffbd02455f5b16a28836157c37edbbd7d77 metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2795901e7f86ddfde453d6c6f4c515b4608f02afb0ffebc217f6d1f76e75fa1f metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 4183293ca0948a62bc5609c8e687c58f2aebb5015a693acfe4a0c84c3fdacbbd46b22d44e94bafeee94e4e1e59dc929cde5fec0f467f623ece8617810445f5ba metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 391eeef64e45451497068dd5e08da5526dc09261 metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 1290f6ee522ff20dfbe311c166e239a66b2695d4cf472ac22ca913b4b8982aa2 metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: a06e1c046bd187d30da601ee5230847ca50e3cd4722f7274033f9fa42f3b359600fa6b78271b80b84927d05b677756afecd891546c105373a7a2d13db9ae38ef metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmp_hi49kn9\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmp5bdr87x6\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/fa09414f-ed1d-4d5f-b17c-ca711545c8f7 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1,\n "nameroot": "a",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1,\n "nameroot": "c",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1,\n "nameroot": "b",\n "nameext": ""\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/b",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1,\n "nameroot": "a",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/a",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1,\n "nameroot": "c",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/c",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1,\n "nameroot": "b",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/b",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n }\n ],\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpu2ojz1u2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpu2ojz1u2,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1tlylhil,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2,target=/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2,readonly \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpl041cwt9/20230605095054-807591.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2 > /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e39ed4a096a3838fe29476728ed1690251cf9fcc metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: b4d7377020d3c1537390509ee07c720ebc847dd48dd479f81e4d76135e2c1f5e metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 483139b37ee1298386820473b14d45c1e81c2454a88959901a5f316639222493a366006aae408898a12fb905c2ad6c635a62f114ad9b7346d5a4a330556e4c31 metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 3ca69e8d6c234a469d16ac28a4a658c92267c423 data/3c/3ca69e8d6c234a469d16ac28a4a658c92267c423\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3ca69e8d6c234a469d16ac28a4a658c92267c423\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n },\n "listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmp2nij54vg\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmp1tlylhil\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpkt9xn476/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe9xc_cpt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu2ojz1u2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkt9xn476\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: c9a6048adf16b96a3869b9d12b8286e0515ae36d metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 939d58de0735b845eeefa4ba7f1c76645eec447303f3b2ae7fab39a9141e6fad metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 6aa596c047b207982f4869bad52eef0dea77db8d82fd9171992d01945bbfbd80800e76ea7018b8bbf86919beef12dcd52dd079a1a7b0705f35f5fc98fd678b21 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 3ac9d7e8c8910108a2ac2f19e44c0e1cf0763451 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 117c9848067265d8ef2fce02241d8e9774f7bca2d12a178683d4827b05478e43 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 493868b27cf007925a3e58ef2cd98597bdd9b0f4e6862644141f079556a33caae08808f96cb8787481cfad9f099ff9562d86c5e8a984eab1c6ed1807d0a76370 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 42c0f1a3661c458606a81f1b63e1b366ca5ed3b5 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 8f2303580e0ce0716d6f0155046cd0e94d484e6524dfded385050b48c300b793 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 48dab132f2cdb691e06380f74c2f7accd0081881124e50c4f38f08cf82e55c231c1611e05cb6f592d97496a13657b96d245c54350d167193fb1b5b9b90f76daf metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 05620a0dfaf1b2d665632f07125d47e98f7df122 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 4f287deb230de31c0d0591206b5e62ef5c8f6ebe124ff22de3fb5a8893bb60e8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 9ade5e90f3c98bc847d54ef557dbee2fb1f12754778362cab0fcf977f70b1f0361e7781fbf117677ade07392a9b69171e755c4636a8ad1ad4f9e2da93d908ef1 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 3199ddc82637a20ecd91da0406042cc741021f2e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 3c8cafd4b517f67bb0fc00cb5e9d75326550804914149c0ca358c59e41ed3d51 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: d39410eb9650f5fcfbfddd101b10bb2dfc717452c2d3e985fdb45b049981151066c8c71f3231b4b69984226f18f2ef72abae04f81ac0448d173fb5728d5b83f5 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: c5ff5ff5b641194487ba00f3df5dd132661fb71a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2f6ebea0ad7601b5fa4ecb3e71edd28daa82f4478ab040ec5c0ee62731cd0eb2 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 12e7b62224e7e8549380e61043b28f6f7a92c047152369eade1d78f53c8cce91e5c734e0a919472e09aaba18c226a2d8052da297eeff5f67b8c17c5335072dc6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': 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[{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}], \'@id\': \'urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 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\'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}], \'@id\': \'urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': 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\'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789\', \'basename\': \'9da56764e3939493b1b27e23e1a15413ad3c7789\', \'nameroot\': \'9da56764e3939493b1b27e23e1a15413ad3c7789\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/3c/3ca69e8d6c234a469d16ac28a4a658c92267c423\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 6\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 1013708c64fb5c51c7ebc74b8a834426cecf9a1f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: f59e18308696286011eb93b7d4f5acf7fb95268e205ced5010e8de2e2a7fb76b workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 77fba2e4a27d69e9eb78969d2ce5fa419d303828fa45f2974e79d9d555e68124cf8277aa7c3a773523b5f9afe4b2431d62ecb49d759cbdcc453514c01454805d workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 5c190af3abd6079fe9da0468818cef0894181ac3 snapshot/directory.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: b2e92881035af88a19765af7e9df298b4016ef43abdd8cde2768230494a6d561 snapshot/directory.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 8803193308dc28ac67e1d538bba1654a7a360e78bf25e71033c277a87f2f10a2643ee86d8cdf73725b7d1021110751f7bc4af4837e95a744d0c37611b09d5552 snapshot/directory.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: bbe97be74e01f68cd004fc10e9b02bde62d75506 metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 5b9a62b72e37e113bcde38bffb56be6551e0173693001915cd9bad0e7d74c6cd metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: a6fc64310c8dafcb54e539e6f25e029bfa7722635d44fbafe52953076fa619c3ae9276c15ad028811e98548096f4b5ae2f0758ae5602c17ba24acd7699fb550a metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e2524a4c4ca0e522cca2b37509d06ea46b20365e metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2f614db0992a28531588c3257650bf7245545bc4f2d5ab971a60f4ed00a01212 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 8f9eefc548aa7137857158666d7d7eceb74f525c8f452b5b5abe433b0e93de184c39397edea61b4e9f99aff6ab5a914f2aaa97b7420efba246e69b8dcf97e575 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: bde438d394d945f9c887bddad2ad0d8162a3af1c bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 454398ea0e8117e9932d5369afd1eb094744c0d157ff620f57b3b965fe65d515 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 197441240163d2867acacff0eab70980a9db59aaaef3d4736472436086ebc064478520bf7917ef56f3fb2c165bcd3d847ca9d23bda182d56fbeffd5125c5edc7 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance')], 'duration': 5.3208884470004705, 'start': 1685951451.105163, 'stop': 1685951456.425921, '$report_type': 'TestReport', 'item_index': 531, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow', 'location': ('tests/test_provenance.py', 169, 'test_directory_workflow'), 'keywords': {'test_directory_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "dir1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1"\n },\n "listing": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0\ntest_directory_workflow0/\n cwltool-run/\n 9da56764e3939493b1b27e23e1a15413ad3c7789\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir2/\n a\n c\n b\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3ca69e8d6c234a469d16ac28a4a658c92267c423\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n metadata/\n directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n manifest.json\n directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n logs/\n engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp9k6tej38/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\n\x1b[1;30mINFO\x1b[0m [workflow _18] start\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmpkt9xn476$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpkt9xn476,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp5bdr87x6,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpijlt4w41/20230605095053-735575.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/ZYBRaV\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpu2ojz1u2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpu2ojz1u2,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1tlylhil,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2,target=/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2,readonly \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpl041cwt9/20230605095054-807591.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2 > /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 042ddf8c8e3a821bd2b1e0b31a7e999d8b6358cf workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 24bbc4fbeba486e56a28be585526c2bfea369513cfd06abeeae6f38289755031 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: adc92e3ab02558f989f144b96d6ff9faf8db91d319f1611c703cb2aaf05062ff6c88fa7376128236b98ba553c2f4e51d88a9cf878fb25a435b907b96318c87f5 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp9k6tej38/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\', \'basename\': \'dir2\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\', \'basename\': \'dir2\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e2a2c4c0c09ac506044b76ffa3081669e50a8ff3 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: d8a50ec3ed7c9940992d5d94ad6f81fe7939d212e7e4267d8999537ea4c1f646 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 3b93050d00a41067c2b8308f1513c3f4c66f1d61d0255c926adb5a4676e5a4174c1764345be25ec811c6c9011799d8427b5f2a9865ee167e4cdd4dd6a30d24f8 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 65d233a8c5869bfb70c5a96f3ccca98fc755c3cd metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 9e0308c4e8c8b0510143d7bc960cfbc97d913a436f42304fb901bf90703192af metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 2ab14b39b928bae6b37bc1b9768a16e683c7b90f7ba46f7fe8c137e1264de2a40e06bfa24120beb97dab2b6fa013ac518d12fcda42bb0f950b8bdf052c1f7107 metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#generate/23607ac8-6d07-4c00-9c5b-47c558e7e9e3 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmpkt9xn476$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpkt9xn476,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp5bdr87x6,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpijlt4w41/20230605095053-735575.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 198893dacc70f008f36bbba2fe29d8535c5bd23c metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 120d87f124da54fd9a263778a81bda3cf1a045665303d8422d7d027a264a647d metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: cf443274e5daf84d8ac240b69e536f9a8017420be7388845de2a8a12a3b31e0500a5e17aae827602fa5214ebb387d8dc1f334530a1fff49734bedeb9185376eb metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 1c8ccffbd02455f5b16a28836157c37edbbd7d77 metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2795901e7f86ddfde453d6c6f4c515b4608f02afb0ffebc217f6d1f76e75fa1f metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 4183293ca0948a62bc5609c8e687c58f2aebb5015a693acfe4a0c84c3fdacbbd46b22d44e94bafeee94e4e1e59dc929cde5fec0f467f623ece8617810445f5ba metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 391eeef64e45451497068dd5e08da5526dc09261 metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 1290f6ee522ff20dfbe311c166e239a66b2695d4cf472ac22ca913b4b8982aa2 metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: a06e1c046bd187d30da601ee5230847ca50e3cd4722f7274033f9fa42f3b359600fa6b78271b80b84927d05b677756afecd891546c105373a7a2d13db9ae38ef metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmp_hi49kn9\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmp5bdr87x6\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/fa09414f-ed1d-4d5f-b17c-ca711545c8f7 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1,\n "nameroot": "a",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1,\n "nameroot": "c",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1,\n "nameroot": "b",\n "nameext": ""\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/b",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1,\n "nameroot": "a",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/a",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1,\n "nameroot": "c",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/c",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1,\n "nameroot": "b",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/b",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n }\n ],\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpu2ojz1u2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpu2ojz1u2,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1tlylhil,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2,target=/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2,readonly \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpl041cwt9/20230605095054-807591.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2 > /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e39ed4a096a3838fe29476728ed1690251cf9fcc metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: b4d7377020d3c1537390509ee07c720ebc847dd48dd479f81e4d76135e2c1f5e metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 483139b37ee1298386820473b14d45c1e81c2454a88959901a5f316639222493a366006aae408898a12fb905c2ad6c635a62f114ad9b7346d5a4a330556e4c31 metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 3ca69e8d6c234a469d16ac28a4a658c92267c423 data/3c/3ca69e8d6c234a469d16ac28a4a658c92267c423\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3ca69e8d6c234a469d16ac28a4a658c92267c423\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n },\n "listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmp2nij54vg\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmp1tlylhil\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpkt9xn476/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe9xc_cpt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu2ojz1u2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkt9xn476\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: c9a6048adf16b96a3869b9d12b8286e0515ae36d metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 939d58de0735b845eeefa4ba7f1c76645eec447303f3b2ae7fab39a9141e6fad metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 6aa596c047b207982f4869bad52eef0dea77db8d82fd9171992d01945bbfbd80800e76ea7018b8bbf86919beef12dcd52dd079a1a7b0705f35f5fc98fd678b21 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 3ac9d7e8c8910108a2ac2f19e44c0e1cf0763451 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 117c9848067265d8ef2fce02241d8e9774f7bca2d12a178683d4827b05478e43 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 493868b27cf007925a3e58ef2cd98597bdd9b0f4e6862644141f079556a33caae08808f96cb8787481cfad9f099ff9562d86c5e8a984eab1c6ed1807d0a76370 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 42c0f1a3661c458606a81f1b63e1b366ca5ed3b5 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 8f2303580e0ce0716d6f0155046cd0e94d484e6524dfded385050b48c300b793 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 48dab132f2cdb691e06380f74c2f7accd0081881124e50c4f38f08cf82e55c231c1611e05cb6f592d97496a13657b96d245c54350d167193fb1b5b9b90f76daf metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 05620a0dfaf1b2d665632f07125d47e98f7df122 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 4f287deb230de31c0d0591206b5e62ef5c8f6ebe124ff22de3fb5a8893bb60e8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 9ade5e90f3c98bc847d54ef557dbee2fb1f12754778362cab0fcf977f70b1f0361e7781fbf117677ade07392a9b69171e755c4636a8ad1ad4f9e2da93d908ef1 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 3199ddc82637a20ecd91da0406042cc741021f2e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 3c8cafd4b517f67bb0fc00cb5e9d75326550804914149c0ca358c59e41ed3d51 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: d39410eb9650f5fcfbfddd101b10bb2dfc717452c2d3e985fdb45b049981151066c8c71f3231b4b69984226f18f2ef72abae04f81ac0448d173fb5728d5b83f5 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: c5ff5ff5b641194487ba00f3df5dd132661fb71a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2f6ebea0ad7601b5fa4ecb3e71edd28daa82f4478ab040ec5c0ee62731cd0eb2 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 12e7b62224e7e8549380e61043b28f6f7a92c047152369eade1d78f53c8cce91e5c734e0a919472e09aaba18c226a2d8052da297eeff5f67b8c17c5335072dc6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}], \'@id\': 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cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 1013708c64fb5c51c7ebc74b8a834426cecf9a1f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: f59e18308696286011eb93b7d4f5acf7fb95268e205ced5010e8de2e2a7fb76b workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 77fba2e4a27d69e9eb78969d2ce5fa419d303828fa45f2974e79d9d555e68124cf8277aa7c3a773523b5f9afe4b2431d62ecb49d759cbdcc453514c01454805d workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 5c190af3abd6079fe9da0468818cef0894181ac3 snapshot/directory.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: b2e92881035af88a19765af7e9df298b4016ef43abdd8cde2768230494a6d561 snapshot/directory.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 8803193308dc28ac67e1d538bba1654a7a360e78bf25e71033c277a87f2f10a2643ee86d8cdf73725b7d1021110751f7bc4af4837e95a744d0c37611b09d5552 snapshot/directory.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: bbe97be74e01f68cd004fc10e9b02bde62d75506 metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 5b9a62b72e37e113bcde38bffb56be6551e0173693001915cd9bad0e7d74c6cd metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: a6fc64310c8dafcb54e539e6f25e029bfa7722635d44fbafe52953076fa619c3ae9276c15ad028811e98548096f4b5ae2f0758ae5602c17ba24acd7699fb550a metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e2524a4c4ca0e522cca2b37509d06ea46b20365e metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2f614db0992a28531588c3257650bf7245545bc4f2d5ab971a60f4ed00a01212 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 8f9eefc548aa7137857158666d7d7eceb74f525c8f452b5b5abe433b0e93de184c39397edea61b4e9f99aff6ab5a914f2aaa97b7420efba246e69b8dcf97e575 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: bde438d394d945f9c887bddad2ad0d8162a3af1c bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 454398ea0e8117e9932d5369afd1eb094744c0d157ff620f57b3b965fe65d515 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 197441240163d2867acacff0eab70980a9db59aaaef3d4736472436086ebc064478520bf7917ef56f3fb2c165bcd3d847ca9d23bda182d56fbeffd5125c5edc7 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance')], 'duration': 0.0009654089999457938, 'start': 1685951456.42858, 'stop': 1685951456.4295459, '$report_type': 'TestReport', 'item_index': 531, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_directory_workflow + location: ('tests/test_provenance.py', 169, 'test_directory_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + when: runtest + nodeid: tests/test_provenance.py::test_directory_workflow + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_no_data_files + location: ('tests/test_provenance.py', 211, 'test_no_data_files') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_no_data_files', 'location': ('tests/test_provenance.py', 211, 'test_no_data_files'), 'keywords': {'test_no_data_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012377330003801035, 'start': 1685951456.4334888, 'stop': 1685951456.434727, '$report_type': 'TestReport', 'item_index': 532, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_input_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "path": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "dirname": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmp_61iiwhz$ cat \\\n /private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/☕😠> /private/tmp/docker_tmp_61iiwhz/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_61iiwhz/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpx9yowb6j\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpyb8f0uu7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp_61iiwhz/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp_61iiwhz\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "path": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "dirname": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmp_61iiwhz$ cat \\\n /private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/☕😠> /private/tmp/docker_tmp_61iiwhz/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_61iiwhz/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpx9yowb6j\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpyb8f0uu7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_61iiwhz/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_61iiwhz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7255514700000276, 'start': 1685951456.1934872, 'stop': 1685951456.919023, '$report_type': 'TestReport', 'item_index': 501, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_input_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "path": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "dirname": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmp_61iiwhz$ cat \\\n /private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/☕😠> /private/tmp/docker_tmp_61iiwhz/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_61iiwhz/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpx9yowb6j\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpyb8f0uu7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp_61iiwhz/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp_61iiwhz\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "path": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "dirname": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmp_61iiwhz$ cat \\\n /private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/☕😠> /private/tmp/docker_tmp_61iiwhz/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_61iiwhz/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpx9yowb6j\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpyb8f0uu7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_61iiwhz/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_61iiwhz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008311599995067809, 'start': 1685951456.9203131, 'stop': 1685951456.9211478, '$report_type': 'TestReport', 'item_index': 501, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u2615\U0001f60d] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u2615\\U0001f60d]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u0627\u0645\u062a\u062d\u0627\u0646] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]'), 'keywords': {'test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.002617494999867631, 'start': 1685951456.923434, 'stop': 1685951456.926054, '$report_type': 'TestReport', 'item_index': 502, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow_no_listing', 'location': ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing'), 'keywords': {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'failed', 'longrepr': {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 891, 'message': "AssertionError: assert not True\n + where True = ()\n + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"}, 'reprtraceback': {'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_directory_workflow_no_listing(tmp_path: Path) -> None:', ' """', ' This test will check for 3 files that should be there and 3 files that should not be there.', ' @param tmp_path:', ' """', ' ', ' dir2 = tmp_path / "dir_deep_listing"', ' dir2.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in a b c ; do echo -n $x | sha1sum ; done', ' "a": "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",', ' "b": "e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",', ' "c": "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",', ' }', ' for x in "abc":', ' # Make test files with predictable hashes', ' with open(dir2 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir3 = tmp_path / "dir_no_listing"', ' dir3.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in d e f ; do echo -n $x | sha1sum ; done', ' "d": "3c363836cf4e16666669a25da280a1865c2d2874",', ' "e": "58e6b3a414a1e090dfc6029add0f3555ccba127f",', ' "f": "4a0a19218e082a343a1b17e5333409af9d98f0f5",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir3 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir4 = tmp_path / "dir_no_info"', ' dir4.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in g h i ; do echo -n $x | sha1sum ; done', ' "g": "54fd1711209fb1c0781092374132c66e79e2241b",', ' "h": "27d5482eebd075de44389774fce28c69f45c8a75",', ' "i": "042dc4512fa3d391c5170cf3aa61e6a638f84342",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir4 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/directory_no_listing.cwl"),', ' "--dir",', ' str(dir2),', ' "--ignore",', ' str(dir3),', ' "--ignore_no_info",', ' str(dir4),', ' )', ' ', ' # Visualize the path structure', ' list_files(tmp_path)', ' ', ' # check invert? as there should be no data in there', ' # check_provenance(folder, directory=True)', ' ', ' # Output should include ls stdout of filenames a b c on each line', ' file_list = (', ' folder', ' / "data"', ' / "84"', ' / "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4"', ' # checksum as returned from:', ' # echo -e "a\\nb\\nc" | sha1sum', ' # 3ca69e8d6c234a469d16ac28a4a658c92267c423 -', ' )', ' # File should not exist...', '> assert not file_list.is_file()', 'E AssertionError: assert not True', "E + where True = ()", "E + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 891, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, 'sections': [], 'chain': [({'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_directory_workflow_no_listing(tmp_path: Path) -> None:', ' """', ' This test will check for 3 files that should be there and 3 files that should not be there.', ' @param tmp_path:', ' """', ' ', ' dir2 = tmp_path / "dir_deep_listing"', ' dir2.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in a b c ; do echo -n $x | sha1sum ; done', ' "a": "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",', ' "b": "e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",', ' "c": "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",', ' }', ' for x in "abc":', ' # Make test files with predictable hashes', ' with open(dir2 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir3 = tmp_path / "dir_no_listing"', ' dir3.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in d e f ; do echo -n $x | sha1sum ; done', ' "d": "3c363836cf4e16666669a25da280a1865c2d2874",', ' "e": "58e6b3a414a1e090dfc6029add0f3555ccba127f",', ' "f": "4a0a19218e082a343a1b17e5333409af9d98f0f5",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir3 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir4 = tmp_path / "dir_no_info"', ' dir4.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in g h i ; do echo -n $x | sha1sum ; done', ' "g": "54fd1711209fb1c0781092374132c66e79e2241b",', ' "h": "27d5482eebd075de44389774fce28c69f45c8a75",', ' "i": "042dc4512fa3d391c5170cf3aa61e6a638f84342",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir4 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/directory_no_listing.cwl"),', ' "--dir",', ' str(dir2),', ' "--ignore",', ' str(dir3),', ' "--ignore_no_info",', ' str(dir4),', ' )', ' ', ' # Visualize the path structure', ' list_files(tmp_path)', ' ', ' # check invert? as there should be no data in there', ' # check_provenance(folder, directory=True)', ' ', ' # Output should include ls stdout of filenames a b c on each line', ' file_list = (', ' folder', ' / "data"', ' / "84"', ' / "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4"', ' # checksum as returned from:', ' # echo -e "a\\nb\\nc" | sha1sum', ' # 3ca69e8d6c234a469d16ac28a4a658c92267c423 -', ' )', ' # File should not exist...', '> assert not file_list.is_file()', 'E AssertionError: assert not True', "E + where True = ()", "E + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 891, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 891, 'message': "AssertionError: assert not True\n + where True = ()\n + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"}, None)]}, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output_1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad"\n },\n "output_2": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0\ntest_directory_workflow_no_lis0/\n cwltool-run/\n 511f5ede99eeae60df68dedf0f5a3c2886774dad\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir_no_info/\n f\n d\n e\n dir_deep_listing/\n a\n c\n b\n dir_no_listing/\n f\n d\n e\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory_no_listing.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3c363836cf4e16666669a25da280a1865c2d2874\n 58/\n 58e6b3a414a1e090dfc6029add0f3555ccba127f\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n a0/\n a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n 4a/\n 4a0a19218e082a343a1b17e5333409af9d98f0f5\n metadata/\n directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n manifest.json\n directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n logs/\n engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/KKDWnh\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'--ignore\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'--ignore_no_info\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: bf9a8c91a428be6becd92c778c02c67d427411a8 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f63ffc058c8cfdb908506337c548afa6df073ae4c60dfd126529041314a548a5 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4fd8262b0744c271fe42c0c7a3142522708348559d0e405bb03bf2ab6becbeb7f64fecd3d8fb0762aa478fd99791200d9c3503e2e2e47b16546bd96fda2bca33 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing"\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}, \'ignore\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}, \'ignore_no_info\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_deep_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_info\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: b8ccdd89c80eca48567812797b860122d330b485 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: c1d4042283d1ce80021fa05c18eed2ae1bffea933f49ddd960b4a09f9a262cb5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: bdc150fa3761c3d002efb9be43f71cf8dac2e1f42259fdff201f185d0603839f2b882baf2cf28656ecfdfa1519fdf92a6b8611fab87b17604c45c09e28ed72ee workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ba113d80556b23c15fd7c2455789b16fe31f2335 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9ae22ea23ca80ffebd84f7e8ff4b640ec2d0f1956c56555485252b0f43892ce6 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 2b38d01f508e3abb2d8249e19be4d222e1b13c37943489f70523fa076f09d012a4f139a3b480706cd411ec961a4f8dcb5b255404f7f71fa74a24bf1886f66889 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 4a0a19218e082a343a1b17e5333409af9d98f0f5 data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 3c363836cf4e16666669a25da280a1865c2d2874 data/3c/3c363836cf4e16666669a25da280a1865c2d2874\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 58e6b3a414a1e090dfc6029add0f3555ccba127f data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 2de598f6b273e2eaaabca9703f0ca739ac4fb4bd metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 803eefe7af4871fc1029330cf00afb4abc33e44591400b6036c887ce4d3516c8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 26f9234c3e7852c13da1a41405bba99f80817d45abf0beed442c3c31cd106afb3b4bdc96fced5ce6e84194af3d156b1c880cef95d9283e3a98f6a87af04e40b8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 94788d2e8451e82a089085ce9a13d21d7648a56a metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: be9b32c701e852c1cce196ed17bb7d04ce147cda1847a2bb31b81a0b3b3bdfb8 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 7f08203a26bde01dd72f0888a87167b6ac571b24e88928de1d73b3cdfcd873e5576f2ccb107b88fa663be20691607e6c74c57f73e2ab5acfa2da3ab1242a5465 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info",\n "basename": "dir_no_info"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from _:c64797b9-0e72-438b-b250-9a183c2486c6 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a01f4d65bf45da813bc5c1482c403b467537faba metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b68aeee0d249094334ad30ea74bf2e8e13de8620ffba8d87dd4ff03f4f707c9 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 0508e90f315884b3b5652850fe11970d60be330ecc6079e443b6f9cf8cdd539ccd6f0f679d05b0ee5c9da1550a3ca81b79425c9b07bca981a24338d10441f318 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 456e3bd591c3db18d15eb03f1b0033f71af12d3a metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 0b6bb416adfdfd452957e1ece6c05a5065835bb85234d7946a264c4016248028 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 856999b9b5ec46248fac41601440d838ba31b12e7c942005522d5e3ef91ebc7edd707457acdfc7d46895a185beb5785592c34d596e22cfb805edc527fc62a209 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9c22bec2e40d921fa850aa5fff207217b2700033 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f8c81c1297aa21b9e5e6d72fbdd4d5bb4dbc5fcc7a8332e4eb07cc6af6620171 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 59200606c8f78dec7b9c4ee540aa62a420c89b773788766589cc20849df29bc5ad624c61cd642b3eb214ab9d94598f99d290690e5e9668690398e7fee40211c3 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmpuu8p9qg8\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmpgouh1jdv\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from _:6798550b-35c6-4878-b539-969960c2ddd6 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "Directory",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n }\n ],\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f"\n }\n },\n {\n "position": [\n 2,\n "ignore"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing",\n "path": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "dirname": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 8cc5feedb2b21504d21859e0f63631f0b517553b metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b0f753abd9f52fa7bda09156130e6b0b936f1cd0705a6894db0eadff26b12a1 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: d6d5e13b344294994185ebcff17d42825d055b22a1e88978298377197522f2542db43987450874f4fd8da234a974070ce23ac03eff61c0a5a647d4c97a68cec6 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 18386d0fde6d11e92ff3eb4475f6553b3093c775 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 31c7501fcee1311e24b50b4142dc0321239dbdaaf821e84c7370321898b234d3 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: be3cf5fc2ba70daafbc4cfe1fe3dd41ee9772f0cccd8f955aa6b0c619abb9eda2bc00818090ad245ffe663fb8151f5b965feb7f4933e3ce68e7d38ff89aa3587 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: a0ce0441f957dcde10291470aa5062ffc7cbdf8c data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "output_1": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n },\n "output_2": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmphgdo2k_m\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmpy12k7j25\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp30294ykg/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe4wl6xjm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp30294ykg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp03q_qnzm\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 831d591ea563d82200f6b29cdbed89958af99946 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8591aab1f32872e19f186118be1462101272c003e5725780ad0a1053b4f45b8 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 1b73e532287cafb4438cfc69dd62ca998d374d25d2d2a9e1aae2d80da74193ec8abc5494227ed037b4a9cbcebd72b4ba2f5c5a995fc9406ad87abc08a421237a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 52917a96deb1331e4f3e0d0c0ca5c06da11b550f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 952621e5f975fa4b8536d1246e03019673efe29716be7dd946885b26420ad858 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 9d13a8b2e9919c7d90a5b65c0af7326c4869efebe2b1525d1dee1d573159349fa8c3d9a06386e6e3054b4517ac86f5389bb90d9cc8105857baa9a142a9958123 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 4660384a529ef8217263414cfe7d8e09a36dae6a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8d43e02f50436e6bc3d92fdf3f37d0452a90fb55cc177c4902b62802ce733b8 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: c3a8205627d56adebcf5e2221b0ce6adc18bebc2af049dbec6dd744c90d1d704cca928860c5b41a8c0fa7056484ca8a454555ab058b982a5a5b3c4b48e35de1d metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: de4b6608f9e3af201c70ff6b53f85749a8492405 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: fadae5349308a66d763eacbe40b6c0348bdfd6947a138a8f8adab6c451836db5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4eb4037e059930960700522093a233245189d1e1284b785d7642142d07ace00ecb89da2a98af756469be68dec3c3b6b0e41368ad4b0325b536fffb642fdc0280 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 153127a4ee5a028d1acd636b0809d434d53da02d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 717a4f8ae33902dcd217991e923892a59b626fe60f616d3cd275806d18e9da4a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 5c8ece230a9c9d65f0b953c27045f92d27e3d6ecc3823e7ef9d3cb4426d66ded6a1fddd45a4bfed846940ed9a1f4bc3f4e9159650a856e9c7bdde1a7162f4ead metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9a047fa31e52f7b66c1a7cebf88c57d9e388c8c6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: a727a73f4d563af8f90316d9ec809d0f853abc53632d2f306ca2944475293cdc metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 83f351fed5f621fa4763e6d0f0762964aa213f325926bf7c406e94eef34970695b9c599bfbd807565b497858edbdfbacc1c3001cbdfb54bb826e49da09ee004f metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'output_1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}, \'output_2\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 153\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a259a2ddea0fb8dbe04ce95431c7b87d74444c8d workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f92dbdf72304f179e312894c469c59f4b08ddabf26264f1ad7a38aa6a527b39e workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 586e6634367c1f8cddf3f26d6e2c7ff826ce3677902c23890028d73f66b854b30eb013b70cecaefb3fdcb8f47fe266e7182f62f24b6f5d94973d73b7dbc04479 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 757937dc88f5d446a6e63c9d1f12acde32b02ecd snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 2c725914f45b19c49b5a6e9540477b70a0273cefdbd82c19de19054de16cb24f snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6d058c8a26fad02c7935f0ee249b186701f49d64ed43f8dccc87ca2f374356b971470006906e36f6d9c888cf50ead1e3fe3f6759e8d1d53a678ca6c1a171387a snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ec85041b357ff2b39338cfbc69d2560640966f89 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 36a504d2c4551667e228d84c4eed90bd73747fe98606b30d912ec9b1ec3767bd metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: f2e20d11de50af96dc8e3bfcd43f0bc8d78342dda00c88c80de92a8f04d4aa3bbf684bf7c59f342cb8ef84393e00327a65b1c107d18f4a449e6116496d5e1f54 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0033518ae68cb74ef1d56196451d0ac9957ce80f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 640cf34ac826eeba52a190d69e5d9f3e0cd8025e6c6a20a5c32c5a479c687c67 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6345ca41b6e0eedc5d3dc2a171ce96cb26aef6a6072f27634478eee2492ac756794ece6fd4949d827a922b55d0d2d7fd5c66b69ade15549c3b96aef4b86e9d0a metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0d2331dab4d408bceb1057cfe5f1e826e1990c29 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 37908e47bb9f9ca212410631fd36ca1f333b9640b281b15639bfc1a822730ba6 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 059ed78b311c6402fb86010caf6283f0bd799fc922264bbef8b82bfb774e14680d16ee89810d4a50f82511d03a2a7596afe8806d3137f4c749d9db1e3b533ca2 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance')], 'duration': 4.963674428999184, 'start': 1685951451.80366, 'stop': 1685951456.767212, '$report_type': 'TestReport', 'item_index': 570, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow_no_listing', 'location': ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing'), 'keywords': {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output_1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad"\n },\n "output_2": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0\ntest_directory_workflow_no_lis0/\n cwltool-run/\n 511f5ede99eeae60df68dedf0f5a3c2886774dad\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir_no_info/\n f\n d\n e\n dir_deep_listing/\n a\n c\n b\n dir_no_listing/\n f\n d\n e\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory_no_listing.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3c363836cf4e16666669a25da280a1865c2d2874\n 58/\n 58e6b3a414a1e090dfc6029add0f3555ccba127f\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n a0/\n a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n 4a/\n 4a0a19218e082a343a1b17e5333409af9d98f0f5\n metadata/\n directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n manifest.json\n directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n logs/\n engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/KKDWnh\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'--ignore\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'--ignore_no_info\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: bf9a8c91a428be6becd92c778c02c67d427411a8 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f63ffc058c8cfdb908506337c548afa6df073ae4c60dfd126529041314a548a5 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4fd8262b0744c271fe42c0c7a3142522708348559d0e405bb03bf2ab6becbeb7f64fecd3d8fb0762aa478fd99791200d9c3503e2e2e47b16546bd96fda2bca33 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing"\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}, \'ignore\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}, \'ignore_no_info\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_deep_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_info\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: b8ccdd89c80eca48567812797b860122d330b485 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: c1d4042283d1ce80021fa05c18eed2ae1bffea933f49ddd960b4a09f9a262cb5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: bdc150fa3761c3d002efb9be43f71cf8dac2e1f42259fdff201f185d0603839f2b882baf2cf28656ecfdfa1519fdf92a6b8611fab87b17604c45c09e28ed72ee workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ba113d80556b23c15fd7c2455789b16fe31f2335 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9ae22ea23ca80ffebd84f7e8ff4b640ec2d0f1956c56555485252b0f43892ce6 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 2b38d01f508e3abb2d8249e19be4d222e1b13c37943489f70523fa076f09d012a4f139a3b480706cd411ec961a4f8dcb5b255404f7f71fa74a24bf1886f66889 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 4a0a19218e082a343a1b17e5333409af9d98f0f5 data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 3c363836cf4e16666669a25da280a1865c2d2874 data/3c/3c363836cf4e16666669a25da280a1865c2d2874\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 58e6b3a414a1e090dfc6029add0f3555ccba127f data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 2de598f6b273e2eaaabca9703f0ca739ac4fb4bd metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 803eefe7af4871fc1029330cf00afb4abc33e44591400b6036c887ce4d3516c8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 26f9234c3e7852c13da1a41405bba99f80817d45abf0beed442c3c31cd106afb3b4bdc96fced5ce6e84194af3d156b1c880cef95d9283e3a98f6a87af04e40b8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 94788d2e8451e82a089085ce9a13d21d7648a56a metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: be9b32c701e852c1cce196ed17bb7d04ce147cda1847a2bb31b81a0b3b3bdfb8 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 7f08203a26bde01dd72f0888a87167b6ac571b24e88928de1d73b3cdfcd873e5576f2ccb107b88fa663be20691607e6c74c57f73e2ab5acfa2da3ab1242a5465 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info",\n "basename": "dir_no_info"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from _:c64797b9-0e72-438b-b250-9a183c2486c6 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a01f4d65bf45da813bc5c1482c403b467537faba metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b68aeee0d249094334ad30ea74bf2e8e13de8620ffba8d87dd4ff03f4f707c9 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 0508e90f315884b3b5652850fe11970d60be330ecc6079e443b6f9cf8cdd539ccd6f0f679d05b0ee5c9da1550a3ca81b79425c9b07bca981a24338d10441f318 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 456e3bd591c3db18d15eb03f1b0033f71af12d3a metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 0b6bb416adfdfd452957e1ece6c05a5065835bb85234d7946a264c4016248028 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 856999b9b5ec46248fac41601440d838ba31b12e7c942005522d5e3ef91ebc7edd707457acdfc7d46895a185beb5785592c34d596e22cfb805edc527fc62a209 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9c22bec2e40d921fa850aa5fff207217b2700033 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f8c81c1297aa21b9e5e6d72fbdd4d5bb4dbc5fcc7a8332e4eb07cc6af6620171 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 59200606c8f78dec7b9c4ee540aa62a420c89b773788766589cc20849df29bc5ad624c61cd642b3eb214ab9d94598f99d290690e5e9668690398e7fee40211c3 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmpuu8p9qg8\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmpgouh1jdv\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from _:6798550b-35c6-4878-b539-969960c2ddd6 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "Directory",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n }\n ],\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f"\n }\n },\n {\n "position": [\n 2,\n "ignore"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing",\n "path": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "dirname": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 8cc5feedb2b21504d21859e0f63631f0b517553b metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b0f753abd9f52fa7bda09156130e6b0b936f1cd0705a6894db0eadff26b12a1 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: d6d5e13b344294994185ebcff17d42825d055b22a1e88978298377197522f2542db43987450874f4fd8da234a974070ce23ac03eff61c0a5a647d4c97a68cec6 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 18386d0fde6d11e92ff3eb4475f6553b3093c775 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 31c7501fcee1311e24b50b4142dc0321239dbdaaf821e84c7370321898b234d3 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: be3cf5fc2ba70daafbc4cfe1fe3dd41ee9772f0cccd8f955aa6b0c619abb9eda2bc00818090ad245ffe663fb8151f5b965feb7f4933e3ce68e7d38ff89aa3587 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: a0ce0441f957dcde10291470aa5062ffc7cbdf8c data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "output_1": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n },\n "output_2": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmphgdo2k_m\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmpy12k7j25\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp30294ykg/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe4wl6xjm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp30294ykg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp03q_qnzm\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 831d591ea563d82200f6b29cdbed89958af99946 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8591aab1f32872e19f186118be1462101272c003e5725780ad0a1053b4f45b8 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 1b73e532287cafb4438cfc69dd62ca998d374d25d2d2a9e1aae2d80da74193ec8abc5494227ed037b4a9cbcebd72b4ba2f5c5a995fc9406ad87abc08a421237a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 52917a96deb1331e4f3e0d0c0ca5c06da11b550f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 952621e5f975fa4b8536d1246e03019673efe29716be7dd946885b26420ad858 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 9d13a8b2e9919c7d90a5b65c0af7326c4869efebe2b1525d1dee1d573159349fa8c3d9a06386e6e3054b4517ac86f5389bb90d9cc8105857baa9a142a9958123 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 4660384a529ef8217263414cfe7d8e09a36dae6a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8d43e02f50436e6bc3d92fdf3f37d0452a90fb55cc177c4902b62802ce733b8 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: c3a8205627d56adebcf5e2221b0ce6adc18bebc2af049dbec6dd744c90d1d704cca928860c5b41a8c0fa7056484ca8a454555ab058b982a5a5b3c4b48e35de1d metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: de4b6608f9e3af201c70ff6b53f85749a8492405 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: fadae5349308a66d763eacbe40b6c0348bdfd6947a138a8f8adab6c451836db5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4eb4037e059930960700522093a233245189d1e1284b785d7642142d07ace00ecb89da2a98af756469be68dec3c3b6b0e41368ad4b0325b536fffb642fdc0280 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 153127a4ee5a028d1acd636b0809d434d53da02d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 717a4f8ae33902dcd217991e923892a59b626fe60f616d3cd275806d18e9da4a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 5c8ece230a9c9d65f0b953c27045f92d27e3d6ecc3823e7ef9d3cb4426d66ded6a1fddd45a4bfed846940ed9a1f4bc3f4e9159650a856e9c7bdde1a7162f4ead metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9a047fa31e52f7b66c1a7cebf88c57d9e388c8c6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: a727a73f4d563af8f90316d9ec809d0f853abc53632d2f306ca2944475293cdc metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 83f351fed5f621fa4763e6d0f0762964aa213f325926bf7c406e94eef34970695b9c599bfbd807565b497858edbdfbacc1c3001cbdfb54bb826e49da09ee004f metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'output_1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}, \'output_2\': {\'location\': 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Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 153\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': 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\'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a259a2ddea0fb8dbe04ce95431c7b87d74444c8d workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f92dbdf72304f179e312894c469c59f4b08ddabf26264f1ad7a38aa6a527b39e workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 586e6634367c1f8cddf3f26d6e2c7ff826ce3677902c23890028d73f66b854b30eb013b70cecaefb3fdcb8f47fe266e7182f62f24b6f5d94973d73b7dbc04479 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 757937dc88f5d446a6e63c9d1f12acde32b02ecd snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 2c725914f45b19c49b5a6e9540477b70a0273cefdbd82c19de19054de16cb24f snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6d058c8a26fad02c7935f0ee249b186701f49d64ed43f8dccc87ca2f374356b971470006906e36f6d9c888cf50ead1e3fe3f6759e8d1d53a678ca6c1a171387a snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ec85041b357ff2b39338cfbc69d2560640966f89 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 36a504d2c4551667e228d84c4eed90bd73747fe98606b30d912ec9b1ec3767bd metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: f2e20d11de50af96dc8e3bfcd43f0bc8d78342dda00c88c80de92a8f04d4aa3bbf684bf7c59f342cb8ef84393e00327a65b1c107d18f4a449e6116496d5e1f54 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0033518ae68cb74ef1d56196451d0ac9957ce80f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 640cf34ac826eeba52a190d69e5d9f3e0cd8025e6c6a20a5c32c5a479c687c67 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6345ca41b6e0eedc5d3dc2a171ce96cb26aef6a6072f27634478eee2492ac756794ece6fd4949d827a922b55d0d2d7fd5c66b69ade15549c3b96aef4b86e9d0a metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0d2331dab4d408bceb1057cfe5f1e826e1990c29 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 37908e47bb9f9ca212410631fd36ca1f333b9640b281b15639bfc1a822730ba6 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 059ed78b311c6402fb86010caf6283f0bd799fc922264bbef8b82bfb774e14680d16ee89810d4a50f82511d03a2a7596afe8806d3137f4c749d9db1e3b533ca2 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance')], 'duration': 0.00152142999922944, 'start': 1685951456.977313, 'stop': 1685951456.978837, '$report_type': 'TestReport', 'item_index': 570, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_directory_workflow_no_listing + location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + when: runtest + nodeid: tests/test_provenance.py::test_directory_workflow_no_listing + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print + location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print', 'location': ('tests/test_rdfprint.py', 10, 'test_rdf_print'), 'keywords': {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003581160008252482, 'start': 1685951456.985954, 'stop': 1685951456.986314, '$report_type': 'TestReport', 'item_index': 571, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_no_data_files', 'location': ('tests/test_provenance.py', 211, 'test_no_data_files'), 'keywords': {'test_no_data_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "required": null\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\'\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\n Source is from\n conditional step\n and may produce\n `null`\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\x1b[0m\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp3p2yoqwz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 76ff7ea1786cf066f9d27f62ce39dc7b8912ff90 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c25c8f928c17d87bf3d643440b193a6526d7ee708caa0c2e46a13d43ebca819f workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 5e670e3ab5fb07cfaf7271c5fd52eb799218d8c263bef6cf5d051ef829c3d5b9ab68c18099ac4c46e1fcc0d29481435a8d1e43f94f1ef389cb2ad25cda86d41c workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nWARNING cwltool:checker.py:319 Workflow checker warning:\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\n Source is from\n conditional step\n and may produce\n `null`\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp3p2yoqwz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {}\nDEBUG cwltool:workflow_job.py:678 [step step1_2] conditional $(self !== null) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step step1_2] inputs was {}\nINFO cwltool:workflow_job.py:744 [step step1_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl#step1/result": null\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {\n "required": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpw85wlbca\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 906879aff073b7271585c8e94b5e786399885ae4 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: a67c7989f08de0b1da9aeab47d3c36cebff617c52e186f7880b52e8589ab0763 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: a6f7ce24e8505d6efaac0991e836abcd8c94ff36b6abc4dd914e5d796e3f848af8e4e45d6fa81d0a292e94c73f30ac9f54cced88dfc7660f3ef20ded961bfd28 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: ef574f04f1f259da4bf821d7a723c4e0b4a16850 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 1aac2b40e29d4704822cf88b89b1a1c81786eb2cdcabfdce8f726584e6a18bac metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: c8fa7ad2a82c832407d2dd830992849721f80759ed32866acc0da5814d61359cf7703a8940a560135068080041eb79eb1284b72b9770ae74e115c926feca9b90 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 5de5a6348852a3f511f4d9b4c19534f843b6949e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 8006f09a7a98c509e354581b676fba851314f3baba8328121fc14fa45937500a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 8e0c7b84d0e4a2e4c1ba883c096d8f28bb358886da2e3e45ff9c7f5eaf60c355cc76bae84bbd07dbbb75f4b675aed8aa88b30ceac0db8af56a81f0f7922b1a97 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: a140d34e45e5963a13fd71358ca866c3d1ae4cfc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c4908a1f885bc4c25a7d1de051db8bb76f7d56cd69ea9d276f6792f6859c21ea metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: e4b03028f42b32b42dd65392b1c89a151ca3dd8d3fdcbaf2a106ddfbd50262d14766ad7ca26fba1d63204f69341ca37f069e148ba8ed04d315e5f0130d9ae303 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: dc447a9373f0695bc582d521621a7f82f4375e71 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c1c43ea92ba15d18b774ee73ffb5efb90e5d4facc26fa73c1b99322905b7d0e8 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: fd9082e819df9611218d883ec13873384a4082cb78d9ba0398d709857a339f2614638d1d428c3ca25c1448ab7b2932b8211f524806636a068befe6473106678b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 3605a04375d7d8d9c81476f2a090fb97cfe82e9e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 31f5626568b9723d0c92ada4c8fecfc29bd0a2cbc02b3a6725a777c8150a36a5 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 1a1d30fb8c9f171c9dfa355e7b42b58d7ff18131c3d3c88988c94002fe70e135f9900c76252cbc5f7fe83bf82829767d078f82071d1dec0bc81aa4a7a0529578 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'required\': None}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: None\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: c6eed93f6f7352dbaf7506c11290ad894b8a0ccc workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 9f3c0380c63d0919594109ffa5689d01ca1e706325627dd1e3f50cf3ccee5537 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: aec8768d19887675932326c35cce2c47d9c8013ab9750434c0f58116e0961efd5d167c421516d18272927ee3872b8cb5b6b4958be528f1cef32c05d51448af9e workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 0080e1d383e12bce874f3ab02b5127e32e49831d snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: f3ecdf078c82fa2b4bd0fcd6c2b8a667fa89defa4b2aa33522458f3877bed805 snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 51b39263588bfca976f0f429659ee9d4249b58f7d81f155a4beb26db5c43d254ffef1174e476666c1d6aa0ec8fc97502fbdc98a24914fc6de5a03c805e5d92bd snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 4306e1682fb3ca36fe69745e655e097c5a8bcd13 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: e92664a105c48f941c9a739505834a3368e5ed6dfd3d1fcbb8d6c40a44da1302 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 6bf26e1d8970422a37e70bb42087eb3df4fadc01f1eac160803014b4294b3b452f1621b4b3a31b3e3e558459024b81091cfdd6cb2eb8c004f38483d0daa18158 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: bce2e1c1aa51e5deabb2d0b32d996772cb0f1960 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 036230af7c59d21808d44fad73d73695b006dcf3195dfd2b0fe26ec3de4d97fc metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 16093a5882ed040e71b229d19014a842d0054e196baefaa8988764bd762db153b19b8606e9cb684c3edca2f0112f2248b7e7530b28c81641fb47b026aefed49c metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 2834064b00c5bb3e2b00dbdbbca5a3106d4b9704 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: f0db42848c92c60010a464280cc2186e58a408c8ecab72421fc7f3b3e09d02cf bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 5b261a0a305476a62385f00004676da3ae873889a94728d0b0b15e992658f4b9b3bb0c50b7895a72b9fe98cbf0ab4616f6c5d2b63f57321ccdec87f8c354b233 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance')], 'duration': 1.032393392000813, 'start': 1685951456.4351192, 'stop': 1685951457.467488, '$report_type': 'TestReport', 'item_index': 532, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_no_data_files', 'location': ('tests/test_provenance.py', 211, 'test_no_data_files'), 'keywords': {'test_no_data_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "required": null\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\'\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\n Source is from\n conditional step\n and may produce\n `null`\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\x1b[0m\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp3p2yoqwz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 76ff7ea1786cf066f9d27f62ce39dc7b8912ff90 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c25c8f928c17d87bf3d643440b193a6526d7ee708caa0c2e46a13d43ebca819f workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 5e670e3ab5fb07cfaf7271c5fd52eb799218d8c263bef6cf5d051ef829c3d5b9ab68c18099ac4c46e1fcc0d29481435a8d1e43f94f1ef389cb2ad25cda86d41c workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nWARNING cwltool:checker.py:319 Workflow checker warning:\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\n Source is from\n conditional step\n and may produce\n `null`\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp3p2yoqwz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {}\nDEBUG cwltool:workflow_job.py:678 [step step1_2] conditional $(self !== null) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step step1_2] inputs was {}\nINFO cwltool:workflow_job.py:744 [step step1_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl#step1/result": null\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {\n "required": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpw85wlbca\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 906879aff073b7271585c8e94b5e786399885ae4 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: a67c7989f08de0b1da9aeab47d3c36cebff617c52e186f7880b52e8589ab0763 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: a6f7ce24e8505d6efaac0991e836abcd8c94ff36b6abc4dd914e5d796e3f848af8e4e45d6fa81d0a292e94c73f30ac9f54cced88dfc7660f3ef20ded961bfd28 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: ef574f04f1f259da4bf821d7a723c4e0b4a16850 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 1aac2b40e29d4704822cf88b89b1a1c81786eb2cdcabfdce8f726584e6a18bac metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: c8fa7ad2a82c832407d2dd830992849721f80759ed32866acc0da5814d61359cf7703a8940a560135068080041eb79eb1284b72b9770ae74e115c926feca9b90 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 5de5a6348852a3f511f4d9b4c19534f843b6949e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 8006f09a7a98c509e354581b676fba851314f3baba8328121fc14fa45937500a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 8e0c7b84d0e4a2e4c1ba883c096d8f28bb358886da2e3e45ff9c7f5eaf60c355cc76bae84bbd07dbbb75f4b675aed8aa88b30ceac0db8af56a81f0f7922b1a97 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: a140d34e45e5963a13fd71358ca866c3d1ae4cfc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c4908a1f885bc4c25a7d1de051db8bb76f7d56cd69ea9d276f6792f6859c21ea metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: e4b03028f42b32b42dd65392b1c89a151ca3dd8d3fdcbaf2a106ddfbd50262d14766ad7ca26fba1d63204f69341ca37f069e148ba8ed04d315e5f0130d9ae303 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: dc447a9373f0695bc582d521621a7f82f4375e71 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c1c43ea92ba15d18b774ee73ffb5efb90e5d4facc26fa73c1b99322905b7d0e8 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: fd9082e819df9611218d883ec13873384a4082cb78d9ba0398d709857a339f2614638d1d428c3ca25c1448ab7b2932b8211f524806636a068befe6473106678b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 3605a04375d7d8d9c81476f2a090fb97cfe82e9e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 31f5626568b9723d0c92ada4c8fecfc29bd0a2cbc02b3a6725a777c8150a36a5 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 1a1d30fb8c9f171c9dfa355e7b42b58d7ff18131c3d3c88988c94002fe70e135f9900c76252cbc5f7fe83bf82829767d078f82071d1dec0bc81aa4a7a0529578 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'required\': None}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: None\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: c6eed93f6f7352dbaf7506c11290ad894b8a0ccc workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 9f3c0380c63d0919594109ffa5689d01ca1e706325627dd1e3f50cf3ccee5537 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: aec8768d19887675932326c35cce2c47d9c8013ab9750434c0f58116e0961efd5d167c421516d18272927ee3872b8cb5b6b4958be528f1cef32c05d51448af9e workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 0080e1d383e12bce874f3ab02b5127e32e49831d snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: f3ecdf078c82fa2b4bd0fcd6c2b8a667fa89defa4b2aa33522458f3877bed805 snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 51b39263588bfca976f0f429659ee9d4249b58f7d81f155a4beb26db5c43d254ffef1174e476666c1d6aa0ec8fc97502fbdc98a24914fc6de5a03c805e5d92bd snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 4306e1682fb3ca36fe69745e655e097c5a8bcd13 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: e92664a105c48f941c9a739505834a3368e5ed6dfd3d1fcbb8d6c40a44da1302 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 6bf26e1d8970422a37e70bb42087eb3df4fadc01f1eac160803014b4294b3b452f1621b4b3a31b3e3e558459024b81091cfdd6cb2eb8c004f38483d0daa18158 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: bce2e1c1aa51e5deabb2d0b32d996772cb0f1960 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 036230af7c59d21808d44fad73d73695b006dcf3195dfd2b0fe26ec3de4d97fc metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 16093a5882ed040e71b229d19014a842d0054e196baefaa8988764bd762db153b19b8606e9cb684c3edca2f0112f2248b7e7530b28c81641fb47b026aefed49c metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 2834064b00c5bb3e2b00dbdbbca5a3106d4b9704 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: f0db42848c92c60010a464280cc2186e58a408c8ecab72421fc7f3b3e09d02cf bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 5b261a0a305476a62385f00004676da3ae873889a94728d0b0b15e992658f4b9b3bb0c50b7895a72b9fe98cbf0ab4616f6c5d2b63f57321ccdec87f8c354b233 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance')], 'duration': 0.0005033320003349218, 'start': 1685951457.468983, 'stop': 1685951457.4694881, '$report_type': 'TestReport', 'item_index': 532, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_no_data_files + location: ('tests/test_provenance.py', 211, 'test_no_data_files') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + when: runtest + nodeid: tests/test_provenance.py::test_no_data_files + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_absolute_path_fails + location: ('tests/test_provenance.py', 616, 'test_absolute_path_fails') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_absolute_path_fails', 'location': ('tests/test_provenance.py', 616, 'test_absolute_path_fails'), 'keywords': {'test_absolute_path_fails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5')], 'duration': 0.004511739999543352, 'start': 1685951457.471474, 'stop': 1685951457.475987, '$report_type': 'TestReport', 'item_index': 533, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_absolute_path_fails', 'location': ('tests/test_provenance.py', 616, 'test_absolute_path_fails'), 'keywords': {'test_absolute_path_fails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5')], 'duration': 0.0004983560002074228, 'start': 1685951457.476467, 'stop': 1685951457.4769669, '$report_type': 'TestReport', 'item_index': 533, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_absolute_path_fails', 'location': ('tests/test_provenance.py', 616, 'test_absolute_path_fails'), 'keywords': {'test_absolute_path_fails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5')], 'duration': 0.0017761660001269775, 'start': 1685951457.477411, 'stop': 1685951457.479188, '$report_type': 'TestReport', 'item_index': 533, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_absolute_path_fails + location: ('tests/test_provenance.py', 616, 'test_absolute_path_fails') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_climboutfails + location: ('tests/test_provenance.py', 621, 'test_climboutfails') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_climboutfails', 'location': ('tests/test_provenance.py', 621, 'test_climboutfails'), 'keywords': {'test_climboutfails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a')], 'duration': 0.004381741000543116, 'start': 1685951457.4802969, 'stop': 1685951457.48468, '$report_type': 'TestReport', 'item_index': 534, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_climboutfails', 'location': ('tests/test_provenance.py', 621, 'test_climboutfails'), 'keywords': {'test_climboutfails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a')], 'duration': 0.0003232019998904434, 'start': 1685951457.4850812, 'stop': 1685951457.485406, '$report_type': 'TestReport', 'item_index': 534, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_climboutfails', 'location': ('tests/test_provenance.py', 621, 'test_climboutfails'), 'keywords': {'test_climboutfails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a')], 'duration': 0.00142488300025434, 'start': 1685951457.4858692, 'stop': 1685951457.487295, '$report_type': 'TestReport', 'item_index': 534, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_climboutfails + location: ('tests/test_provenance.py', 621, 'test_climboutfails') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_writable_string + location: ('tests/test_provenance.py', 626, 'test_writable_string') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_writable_string', 'location': ('tests/test_provenance.py', 626, 'test_writable_string'), 'keywords': {'test_writable_string': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h')], 'duration': 0.0051495199995770236, 'start': 1685951457.488235, 'stop': 1685951457.493385, '$report_type': 'TestReport', 'item_index': 535, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_writable_string', 'location': ('tests/test_provenance.py', 626, 'test_writable_string'), 'keywords': {'test_writable_string': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha1.txt: 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha256.txt: 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha512.txt: c2bad2223811194582af4d1508ac02cd69eeeeedeeb98d54fcae4dcefb13cc882e7640328206603d3fb9cd5f949a9be0db054dd34fbfa190c498a5fe09750cef file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha1.txt: 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha256.txt: 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha512.txt: c2bad2223811194582af4d1508ac02cd69eeeeedeeb98d54fcae4dcefb13cc882e7640328206603d3fb9cd5f949a9be0db054dd34fbfa190c498a5fe09750cef file.txt')], 'duration': 0.0022833869998066803, 'start': 1685951457.4939451, 'stop': 1685951457.49623, '$report_type': 'TestReport', 'item_index': 535, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_writable_string', 'location': ('tests/test_provenance.py', 626, 'test_writable_string'), 'keywords': {'test_writable_string': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha1.txt: 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha256.txt: 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha512.txt: c2bad2223811194582af4d1508ac02cd69eeeeedeeb98d54fcae4dcefb13cc882e7640328206603d3fb9cd5f949a9be0db054dd34fbfa190c498a5fe09750cef file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha1.txt: 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha256.txt: 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha512.txt: c2bad2223811194582af4d1508ac02cd69eeeeedeeb98d54fcae4dcefb13cc882e7640328206603d3fb9cd5f949a9be0db054dd34fbfa190c498a5fe09750cef file.txt'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h')], 'duration': 0.0020307000004322617, 'start': 1685951457.49675, 'stop': 1685951457.498782, '$report_type': 'TestReport', 'item_index': 535, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_writable_string + location: ('tests/test_provenance.py', 626, 'test_writable_string') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_writable_unicode_string + location: ('tests/test_provenance.py', 658, 'test_writable_unicode_string') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_writable_unicode_string', 'location': ('tests/test_provenance.py', 658, 'test_writable_unicode_string'), 'keywords': {'test_writable_unicode_string': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d')], 'duration': 0.0037396589996205876, 'start': 1685951457.5008562, 'stop': 1685951457.504597, '$report_type': 'TestReport', 'item_index': 536, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_writable_unicode_string', 'location': ('tests/test_provenance.py', 658, 'test_writable_unicode_string'), 'keywords': {'test_writable_unicode_string': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha256.txt: bb16a101c183c6c35bd53683d04273e214e77926e039369f065b11df84b47c80 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha512.txt: e03ebad752a05a76268c9516807e8564af9a26827485e1e3525b06e1d784437a5e9455f764a9914f1a7b851ebfeab27127a5174955711b7e4fd2bfaa8057bd1b file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha256.txt: bb16a101c183c6c35bd53683d04273e214e77926e039369f065b11df84b47c80 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha512.txt: e03ebad752a05a76268c9516807e8564af9a26827485e1e3525b06e1d784437a5e9455f764a9914f1a7b851ebfeab27127a5174955711b7e4fd2bfaa8057bd1b file.txt')], 'duration': 0.00224830600018322, 'start': 1685951457.5051498, 'stop': 1685951457.5073988, '$report_type': 'TestReport', 'item_index': 536, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_writable_unicode_string', 'location': ('tests/test_provenance.py', 658, 'test_writable_unicode_string'), 'keywords': {'test_writable_unicode_string': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha256.txt: bb16a101c183c6c35bd53683d04273e214e77926e039369f065b11df84b47c80 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha512.txt: e03ebad752a05a76268c9516807e8564af9a26827485e1e3525b06e1d784437a5e9455f764a9914f1a7b851ebfeab27127a5174955711b7e4fd2bfaa8057bd1b file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha256.txt: bb16a101c183c6c35bd53683d04273e214e77926e039369f065b11df84b47c80 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha512.txt: e03ebad752a05a76268c9516807e8564af9a26827485e1e3525b06e1d784437a5e9455f764a9914f1a7b851ebfeab27127a5174955711b7e4fd2bfaa8057bd1b file.txt'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d')], 'duration': 0.002243257999907655, 'start': 1685951457.507967, 'stop': 1685951457.5102122, '$report_type': 'TestReport', 'item_index': 536, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_writable_unicode_string + location: ('tests/test_provenance.py', 658, 'test_writable_unicode_string') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_secrets.py::test_secret_workflow_log_override + location: ('tests/test_secrets.py', 101, 'test_secret_workflow_log_override') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log_override', 'location': ('tests/test_secrets.py', 101, 'test_secret_workflow_log_override'), 'keywords': {'test_secret_workflow_log_override': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00023334999968938064, 'start': 1685951457.511599, 'stop': 1685951457.5118332, '$report_type': 'TestReport', 'item_index': 585, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]'), 'keywords': {'test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "path": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "dirname": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj3ojtpk2$ cat \\\n /private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/امتحان > /private/tmp/docker_tmpj3ojtpk2/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj3ojtpk2/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmpe7iqwjai\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmpq5u7xb8a\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj3ojtpk2/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj3ojtpk2\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "path": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "dirname": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj3ojtpk2$ cat \\\n /private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/امتحان > /private/tmp/docker_tmpj3ojtpk2/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj3ojtpk2/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmpe7iqwjai\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmpq5u7xb8a\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj3ojtpk2/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj3ojtpk2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.718482084000243, 'start': 1685951456.926538, 'stop': 1685951457.645005, '$report_type': 'TestReport', 'item_index': 502, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]'), 'keywords': {'test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "path": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "dirname": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj3ojtpk2$ cat \\\n /private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/امتحان > /private/tmp/docker_tmpj3ojtpk2/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj3ojtpk2/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmpe7iqwjai\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmpq5u7xb8a\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj3ojtpk2/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj3ojtpk2\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "path": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "dirname": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj3ojtpk2$ cat \\\n /private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/امتحان > /private/tmp/docker_tmpj3ojtpk2/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj3ojtpk2/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmpe7iqwjai\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmpq5u7xb8a\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj3ojtpk2/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj3ojtpk2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008691729999554809, 'start': 1685951457.6467788, 'stop': 1685951457.647649, '$report_type': 'TestReport', 'item_index': 502, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u0627\u0645\u062a\u062d\u0627\u0646] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[abc+DEFGZ.z_12345-] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[abc+DEFGZ.z_12345-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_input_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016044889998738654, 'start': 1685951457.65006, 'stop': 1685951457.651665, '$report_type': 'TestReport', 'item_index': 503, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print', 'location': ('tests/test_rdfprint.py', 10, 'test_rdf_print'), 'keywords': {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '@prefix CommandLineBinding: .\n@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n cwl:inputBinding [ CommandLineBinding:position 1 ] ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'")], 'duration': 0.6995283690002907, 'start': 1685951456.986822, 'stop': 1685951457.686334, '$report_type': 'TestReport', 'item_index': 571, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print', 'location': ('tests/test_rdfprint.py', 10, 'test_rdf_print'), 'keywords': {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '@prefix CommandLineBinding: .\n@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n cwl:inputBinding [ CommandLineBinding:position 1 ] ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'")], 'duration': 0.00019048600006499328, 'start': 1685951457.686794, 'stop': 1685951457.686985, '$report_type': 'TestReport', 'item_index': 571, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print + location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print_unicode + location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print_unicode', 'location': ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode'), 'keywords': {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005043370001658332, 'start': 1685951457.688944, 'stop': 1685951457.68945, '$report_type': 'TestReport', 'item_index': 572, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log', 'location': ('tests/test_secrets.py', 59, 'test_secret_workflow_log'), 'keywords': {'test_secret_workflow_log': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "path": "/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19"\n }\n}'), ('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl",\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_job.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "example.conf"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job step1] initial work dir {\n "_:a013850b-7da3-40b4-b8b0-9956d7c5d457": [\n "username: user\\npassword: (secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)\\n",\n "/YZQNYw/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp1kf06cap$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp1kf06cap,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp0hnprorq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpxnlrl83i/20230605095056-771506.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/debian:stable-slim \\\n cat \\\n example.conf > /private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpjged9yh3\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmp0hnprorq\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1kf06cap\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp36ys10ak\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 3.3611989219998577, 'start': 1685951454.434431, 'stop': 1685951457.795549, '$report_type': 'TestReport', 'item_index': 583, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log', 'location': ('tests/test_secrets.py', 59, 'test_secret_workflow_log'), 'keywords': {'test_secret_workflow_log': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "path": "/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19"\n }\n}'), ('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl",\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_job.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "example.conf"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job step1] initial work dir {\n "_:a013850b-7da3-40b4-b8b0-9956d7c5d457": [\n "username: user\\npassword: (secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)\\n",\n "/YZQNYw/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp1kf06cap$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp1kf06cap,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp0hnprorq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpxnlrl83i/20230605095056-771506.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/debian:stable-slim \\\n cat \\\n example.conf > /private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpjged9yh3\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmp0hnprorq\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1kf06cap\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp36ys10ak\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00046288000066851964, 'start': 1685951457.797031, 'stop': 1685951457.7974951, '$report_type': 'TestReport', 'item_index': 583, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_secrets.py::test_secret_workflow_log + location: ('tests/test_secrets.py', 59, 'test_secret_workflow_log') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_secrets.py::test_secret_workflow_log_singularity + location: ('tests/test_secrets.py', 80, 'test_secret_workflow_log_singularity') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log_singularity', 'location': ('tests/test_secrets.py', 80, 'test_secret_workflow_log_singularity'), 'keywords': {'test_secret_workflow_log_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_secrets.py', 81, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003086459992118762, 'start': 1685951457.800096, 'stop': 1685951457.800406, '$report_type': 'TestReport', 'item_index': 584, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log_singularity', 'location': ('tests/test_secrets.py', 80, 'test_secret_workflow_log_singularity'), 'keywords': {'test_secret_workflow_log_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003312149992780178, 'start': 1685951457.801483, 'stop': 1685951457.801816, '$report_type': 'TestReport', 'item_index': 584, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_secrets.py::test_secret_workflow_log_singularity + location: ('tests/test_secrets.py', 80, 'test_secret_workflow_log_singularity') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity.py::test_singularity2_docker_image_id_in_tool + location: ('tests/test_singularity.py', 114, 'test_singularity2_docker_image_id_in_tool') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity2_docker_image_id_in_tool', 'location': ('tests/test_singularity.py', 114, 'test_singularity2_docker_image_id_in_tool'), 'keywords': {'test_singularity2_docker_image_id_in_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 115, 'Skipped: Requires that version 2.6.x of singularity executable version is on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00026410500049678376, 'start': 1685951457.802933, 'stop': 1685951457.803199, '$report_type': 'TestReport', 'item_index': 591, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity2_docker_image_id_in_tool', 'location': ('tests/test_singularity.py', 114, 'test_singularity2_docker_image_id_in_tool'), 'keywords': {'test_singularity2_docker_image_id_in_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0001863429997683852, 'start': 1685951457.803916, 'stop': 1685951457.8041039, '$report_type': 'TestReport', 'item_index': 591, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_singularity.py::test_singularity2_docker_image_id_in_tool + location: ('tests/test_singularity.py', 114, 'test_singularity2_docker_image_id_in_tool') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity.py::test_singularity3_docker_image_id_in_tool + location: ('tests/test_singularity.py', 138, 'test_singularity3_docker_image_id_in_tool') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity3_docker_image_id_in_tool', 'location': ('tests/test_singularity.py', 138, 'test_singularity3_docker_image_id_in_tool'), 'keywords': {'test_singularity3_docker_image_id_in_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 139, 'Skipped: Requires that version 3.x of singularity executable version is on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002477910002198769, 'start': 1685951457.804945, 'stop': 1685951457.805194, '$report_type': 'TestReport', 'item_index': 592, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity3_docker_image_id_in_tool', 'location': ('tests/test_singularity.py', 138, 'test_singularity3_docker_image_id_in_tool'), 'keywords': {'test_singularity3_docker_image_id_in_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003100769999946351, 'start': 1685951457.805884, 'stop': 1685951457.806195, '$report_type': 'TestReport', 'item_index': 592, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_singularity.py::test_singularity3_docker_image_id_in_tool + location: ('tests/test_singularity.py', 138, 'test_singularity3_docker_image_id_in_tool') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity_versions.py::test_get_version + location: ('tests/test_singularity_versions.py', 32, 'test_get_version') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity_versions.py::test_get_version', 'location': ('tests/test_singularity_versions.py', 32, 'test_get_version'), 'keywords': {'test_get_version': 1, 'test_singularity_versions.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002954239998871344, 'start': 1685951457.808606, 'stop': 1685951457.808903, '$report_type': 'TestReport', 'item_index': 593, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity_versions.py::test_get_version', 'location': ('tests/test_singularity_versions.py', 32, 'test_get_version'), 'keywords': {'test_get_version': 1, 'test_singularity_versions.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 1.0.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 3.8.5 ({_SINGULARITY_FLAVOR}.\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:singularity.py:58 Singularity version: 1.0.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 3.8.5 ({_SINGULARITY_FLAVOR}.')], 'duration': 0.0012486929999795393, 'start': 1685951457.809377, 'stop': 1685951457.810627, '$report_type': 'TestReport', 'item_index': 593, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity_versions.py::test_get_version', 'location': ('tests/test_singularity_versions.py', 32, 'test_get_version'), 'keywords': {'test_get_version': 1, 'test_singularity_versions.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 1.0.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 3.8.5 ({_SINGULARITY_FLAVOR}.\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:singularity.py:58 Singularity version: 1.0.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 3.8.5 ({_SINGULARITY_FLAVOR}.')], 'duration': 0.00018926099983218592, 'start': 1685951457.811023, 'stop': 1685951457.811213, '$report_type': 'TestReport', 'item_index': 593, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity_versions.py::test_version_checks', 'location': ('tests/test_singularity_versions.py', 61, 'test_version_checks'), 'keywords': {'test_version_checks': 1, 'test_singularity_versions.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0001906059997054399, 'start': 1685951457.812039, 'stop': 1685951457.8122308, '$report_type': 'TestReport', 'item_index': 594, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity_versions.py::test_version_checks + location: ('tests/test_singularity_versions.py', 61, 'test_version_checks') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity_versions.py::test_version_checks', 'location': ('tests/test_singularity_versions.py', 61, 'test_version_checks'), 'keywords': {'test_version_checks': 1, 'test_singularity_versions.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 1.0.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 0.0.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 0.0.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 0.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 2.6 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 3.0 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 3.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 3.4 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 3.6.3 ({_SINGULARITY_FLAVOR}.\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:singularity.py:58 Singularity version: 1.0.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 0.0.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 0.0.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 0.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 2.6 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 3.0 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 3.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 3.4 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 3.6.3 ({_SINGULARITY_FLAVOR}.')], 'duration': 0.0020836470002905116, 'start': 1685951457.8125498, 'stop': 1685951457.814636, '$report_type': 'TestReport', 'item_index': 594, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity_versions.py::test_version_checks', 'location': ('tests/test_singularity_versions.py', 61, 'test_version_checks'), 'keywords': {'test_version_checks': 1, 'test_singularity_versions.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 1.0.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 0.0.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 0.0.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 0.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 2.6 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 3.0 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 3.1 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 3.4 ({_SINGULARITY_FLAVOR}.\x1b[0m\n\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 3.6.3 ({_SINGULARITY_FLAVOR}.\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:singularity.py:58 Singularity version: 1.0.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 0.0.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 0.0.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 0.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 2.6 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 3.0 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 3.1 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 3.4 ({_SINGULARITY_FLAVOR}.\nDEBUG cwltool:singularity.py:58 Singularity version: 3.6.3 ({_SINGULARITY_FLAVOR}.')], 'duration': 0.0003415829996811226, 'start': 1685951457.815315, 'stop': 1685951457.815658, '$report_type': 'TestReport', 'item_index': 594, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: +\ð/\0^]°=_ð#\°Óm0=SðŸX0±\0?SðŸXðXTð#\ðwT°JTðŸXðI^ðõYð]]0±\ðXT0?SðŸXðwT°JTð/\°=_°Ám0=SðŸX0¹Q0FT pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_singularity_versions.py::test_version_checks + location: ('tests/test_singularity_versions.py', 61, 'test_version_checks') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_output + location: ('tests/test_stdout_stderr_log_dir.py', 6, 'test_log_dir_echo_output') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_output', 'location': ('tests/test_stdout_stderr_log_dir.py', 6, 'test_log_dir_echo_output'), 'keywords': {'test_log_dir_echo_output': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0019657180000649532, 'start': 1685951457.8169448, 'stop': 1685951457.818912, '$report_type': 'TestReport', 'item_index': 595, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_input_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "path": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "dirname": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_7] /private/tmp/docker_tmpb7jiejr4$ cat \\\n /private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345- > /private/tmp/docker_tmpb7jiejr4/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpb7jiejr4/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] Removing input staging directory /private/tmp/docker_tmpbm414g78\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] Removing temporary directory /private/tmp/docker_tmp4f26hj3w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpb7jiejr4/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpb7jiejr4\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_7] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_7] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_7] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "path": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "dirname": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_7] initial work dir {}\nINFO cwltool:job.py:266 [job script_7] /private/tmp/docker_tmpb7jiejr4$ cat \\\n /private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345- > /private/tmp/docker_tmpb7jiejr4/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_7] completed success\nDEBUG cwltool:job.py:422 [job script_7] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpb7jiejr4/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_7] Removing input staging directory /private/tmp/docker_tmpbm414g78\nDEBUG cwltool:job.py:454 [job script_7] Removing temporary directory /private/tmp/docker_tmp4f26hj3w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpb7jiejr4/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpb7jiejr4\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.654889022000134, 'start': 1685951457.652152, 'stop': 1685951458.3070269, '$report_type': 'TestReport', 'item_index': 503, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_input_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "path": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "dirname": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_7] /private/tmp/docker_tmpb7jiejr4$ cat \\\n /private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345- > /private/tmp/docker_tmpb7jiejr4/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpb7jiejr4/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] Removing input staging directory /private/tmp/docker_tmpbm414g78\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] Removing temporary directory /private/tmp/docker_tmp4f26hj3w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpb7jiejr4/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpb7jiejr4\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_7] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_7] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_7] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "path": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "dirname": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_7] initial work dir {}\nINFO cwltool:job.py:266 [job script_7] /private/tmp/docker_tmpb7jiejr4$ cat \\\n /private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345- > /private/tmp/docker_tmpb7jiejr4/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_7] completed success\nDEBUG cwltool:job.py:422 [job script_7] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpb7jiejr4/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_7] Removing input staging directory /private/tmp/docker_tmpbm414g78\nDEBUG cwltool:job.py:454 [job script_7] Removing temporary directory /private/tmp/docker_tmp4f26hj3w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpb7jiejr4/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpb7jiejr4\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007895850003478699, 'start': 1685951458.308804, 'stop': 1685951458.3095949, '$report_type': 'TestReport', 'item_index': 503, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_input_files[abc+DEFGZ.z_12345-] + location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[abc+DEFGZ.z_12345-]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u6e2c\u8a66] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u6e2c\\u8a66]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u6e2c\\u8a66]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u6e2c\\u8a66]'), 'keywords': {'test_unicode_in_output_files[\\u6e2c\\u8a66]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u6e2c\\u8a66': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001846268000008422, 'start': 1685951458.312243, 'stop': 1685951458.31409, '$report_type': 'TestReport', 'item_index': 504, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_output', 'location': ('tests/test_stdout_stderr_log_dir.py', 6, 'test_log_dir_echo_output'), 'keywords': {'test_log_dir_echo_output': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl] {\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n "inp"\n ],\n "datum": "hello"\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl] /private/tmp/docker_tmpwfwddvpw$ echo \\\n hello > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_log_dir_echo_output0/echo.cwl/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl] outputs {\n "out": "hello\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl] Removing input staging directory /private/tmp/docker_tmp55k4p0um\nDEBUG cwltool:job.py:454 [job echo.cwl] Removing temporary directory /private/tmp/docker_tmpaxet3r4x\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwfwddvpw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7238111329997992, 'start': 1685951457.819371, 'stop': 1685951458.5431669, '$report_type': 'TestReport', 'item_index': 595, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_output', 'location': ('tests/test_stdout_stderr_log_dir.py', 6, 'test_log_dir_echo_output'), 'keywords': {'test_log_dir_echo_output': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl] {\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n "inp"\n ],\n "datum": "hello"\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl] /private/tmp/docker_tmpwfwddvpw$ echo \\\n hello > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_log_dir_echo_output0/echo.cwl/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl] outputs {\n "out": "hello\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl] Removing input staging directory /private/tmp/docker_tmp55k4p0um\nDEBUG cwltool:job.py:454 [job echo.cwl] Removing temporary directory /private/tmp/docker_tmpaxet3r4x\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwfwddvpw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000621432999651006, 'start': 1685951458.544076, 'stop': 1685951458.544699, '$report_type': 'TestReport', 'item_index': 595, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_output + location: ('tests/test_stdout_stderr_log_dir.py', 6, 'test_log_dir_echo_output') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_no_output + location: ('tests/test_stdout_stderr_log_dir.py', 22, 'test_log_dir_echo_no_output') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_no_output', 'location': ('tests/test_stdout_stderr_log_dir.py', 22, 'test_log_dir_echo_no_output'), 'keywords': {'test_log_dir_echo_no_output': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001245518999894557, 'start': 1685951458.546586, 'stop': 1685951458.5478332, '$report_type': 'TestReport', 'item_index': 596, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow', 'location': ('tests/test_provenance.py', 74, 'test_revsort_workflow'), 'keywords': {'test_revsort_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "sorted_output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt",\n "basename": "output.txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step rev\n\x1b[1;30mINFO\x1b[0m [step rev] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\n\x1b[1;30mINFO\x1b[0m [job rev] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job rev] completed success\n\x1b[1;30mINFO\x1b[0m [step rev] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step sorted\n\x1b[1;30mINFO\x1b[0m [step sorted] start\n\x1b[1;30mINFO\x1b[0m [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\n\x1b[1;30mINFO\x1b[0m [job sorted] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job sorted] completed success\n\x1b[1;30mINFO\x1b[0m [step sorted] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\', job_order=[\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}, \'reverse_sort\': True}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b9792322151224743947536605dc9cca24e185d8 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 0b54605194d27895bfbccb163d89b64dba40161d9771e915b204ef89c0501446 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 924e606ff3341e4daea625839633159c1a0c71d12d64532f78160aa03284c5537f3726613c5fa3ec938e0cb3972113e20f4fde6617c88cc98f7e6ec6001e31b5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n },\n "reverse_sort": true\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step rev\nDEBUG cwltool:workflow_job.py:727 [step rev] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step rev] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step rev] start\nDEBUG cwltool:command_line_tool.py:982 [job rev] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/revtool.cwl as part of step rev\nDEBUG cwltool:command_line_tool.py:988 [job rev] {\n "revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job rev] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job rev] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "revtool_input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "dirname": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job rev] initial work dir {}\nINFO cwltool:job.py:266 [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:job.py:905 [job rev] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 97fe1b50b4582cebc7d853796ebd62e3e163aa3f data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nINFO cwltool:job.py:419 [job rev] completed success\nDEBUG cwltool:job.py:422 [job rev] outputs {\n "revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step rev] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:572 [step rev] completed success\nDEBUG cwltool:job.py:446 [job rev] Removing input staging directory /private/tmp/docker_tmp0onaxo3l\nDEBUG cwltool:job.py:454 [job rev] Removing temporary directory /private/tmp/docker_tmpwl097n7z\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step sorted\nDEBUG cwltool:workflow_job.py:727 [step sorted] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step sorted] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:75 [step sorted] start\nDEBUG cwltool:command_line_tool.py:982 [job sorted] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sorttool.cwl as part of step sorted\nDEBUG cwltool:command_line_tool.py:988 [job sorted] {\n "reverse": true,\n "sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job sorted] path mappings is {\n "file:///private/tmp/docker_tmpo8j3qsh0/output.txt": [\n "/private/tmp/docker_tmpo8j3qsh0/output.txt",\n "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job sorted] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sort"\n },\n {\n "position": [\n 1,\n "reverse"\n ],\n "prefix": "--reverse",\n "datum": true\n },\n {\n "position": [\n 2,\n "sorted_input"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1",\n "path": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "dirname": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job sorted] initial work dir {}\nINFO cwltool:job.py:266 [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\nINFO cwltool:job.py:905 [job sorted] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: b9214658cc453331b62c2282b772a5c063dbd284 data/b9/b9214658cc453331b62c2282b772a5c063dbd284\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nINFO cwltool:job.py:419 [job sorted] completed success\nDEBUG cwltool:job.py:422 [job sorted] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step sorted] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step sorted] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:job.py:446 [job sorted] Removing input staging directory /private/tmp/docker_tmpt9i2u3d_\nDEBUG cwltool:job.py:454 [job sorted] Removing temporary directory /private/tmp/docker_tmp7ypgmrbr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplkmwaaf_/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplkmwaaf_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp46e4pq4y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo8j3qsh0\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: df915edbd6b5e75857277eb6c8e1377f0d051ef1 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4e56225fad8da955eebc34f2c094def00b9a7b6b39c500bd4ba036618c22e6f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 42a067ea2914371f209f8c25161dee0d1589e739c64f3275519f23d0af480afc636ea8b3298663632e89b2033c18a855ad9eb5290298ed00837688a946ac1523 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 553157706bf95e14c524a396a623d0f3f87f8ecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c6eccb1bc96bd4f55d03be6f4c0262a736dd8296ecae60d0d403bc9bfc8ca92b metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: f8c2586c8f0749fe5ef9e772f752c63acc2ba9dc8176e2cd8da9e677b952f7ba5a8410f062937ee19a3db25b2a414ef3566294dec7e6b6d011f21d176f3e4e3f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: ca44d2cee82bdf4159a998516a8b7d97de4becde metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 9abbc3a964398906a0a6c446f05be412b4f818c5df80213eefb95585644407f9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4dd04bc545f060056ec3c0eb38c22e70e30c30f4b3d633c60a802e4fcb4607737e7938f57b1eaea5a7044b23bf39461a15ccd68a344564b0a257cb7c966d8562 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b52bb0536caa8678dee76e093bab66c9f6ab72d8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fe046d6822ede74b785f00faa9e38aeeb92d573926c5e8f0dc3e87ddcf655336 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 3fe06b96dca53c5afed7eee93e58b27dd8330c34ce5436271af797259e4ffbc9790bb32f8cdab7244e1a83d0f8f1137464dc0dd757d841ac69412932cf09a9f9 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e58bcf95cb06e3d42132d9c488c389eb62de0170 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 27f34aff0b66f02249b46599489c42e37efc5de28e05274bba403a11a31bd86e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4f70440a6e4c80363471248e4d36d4df1a61f6bdeebdc41391bab98dcc5715361142776d4dd4dcc2b9f81d4687b83ea3a259c4a52374d0e6bed988bb6cfc8683 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: bb4d8f1c88da465df4d205fe71778cf5ee0c971e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 45e8790efb18825deb4c136d97032976f831b167076b31e43bd6ae66fc7466d7 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: bad9c61094a072702da2befe78c06dc406039eba8d4f5abeb39fb0646589428829d6e32ce91b705be4d0b9eba94cad5ca02e0665a23e9190438ef61b05611244 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'sorted_output\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 0536da382206c737b78578fb4cd56d470854cb65 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: ca8f0addfb91188dc24d6f6f2455b58ba794fa05417a99e239993ca8a25627c4 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 1ecd7b38f4685c4c7c7a124deaf30613ef849999f7aa5afb3b537d294a9e66933052c4e35fcb2d7a37e565e33a918c497349b9fc901cf828c5f9cd592dce1114 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: eac590a030efa84e4abe5c70bfbbe059d59cb909 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c85344af5e84a113da5636b4c42935c478fe1b587b2f84f82aa07465a71ce1d1 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fc05d8795084ee56e93edfd135c625c462e71dfaed99a7dc613264eb2b8a75a518580a187fb580fa9309c4cb1398a6501040c6251a221f31cbe67c5576a5d799 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: a7199d53b1f707ab9bfa7a88f832a843a05da1b5 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 44dad89d06c949f171fb43e2c2a870f92520a7d288460cafadfd19afefb7697c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fed9bf631358efdec9cb96154215b41a76dc6b7cd38eeb794f6a94212e5fcf868dcc776b0cec9d950de8370d3e4399a7c36833da2d5bdebfb0e193d813047ad4 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 825bbdb1ae0c5b4dab6115409f478fd2b7546ef1 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 65c5c5444143e944a90a7ec7fed5e89f3b4195f53a84f0747bca4875ad8602ec bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 9212abe820053e53692266203ba3819ceae75bb7f5d82f74281d7d1e9e0682ee506d9b210ef2d2bae5396e8d0f751bafbdf1f361747bf3cdc4d9aaa247919f25 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance')], 'duration': 4.937757239000348, 'start': 1685951453.6408331, 'stop': 1685951458.578468, '$report_type': 'TestReport', 'item_index': 525, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow', 'location': ('tests/test_provenance.py', 74, 'test_revsort_workflow'), 'keywords': {'test_revsort_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "sorted_output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt",\n "basename": "output.txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step rev\n\x1b[1;30mINFO\x1b[0m [step rev] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\n\x1b[1;30mINFO\x1b[0m [job rev] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job rev] completed success\n\x1b[1;30mINFO\x1b[0m [step rev] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step sorted\n\x1b[1;30mINFO\x1b[0m [step sorted] start\n\x1b[1;30mINFO\x1b[0m [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\n\x1b[1;30mINFO\x1b[0m [job sorted] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job sorted] completed success\n\x1b[1;30mINFO\x1b[0m [step sorted] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\', job_order=[\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}, \'reverse_sort\': True}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b9792322151224743947536605dc9cca24e185d8 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 0b54605194d27895bfbccb163d89b64dba40161d9771e915b204ef89c0501446 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 924e606ff3341e4daea625839633159c1a0c71d12d64532f78160aa03284c5537f3726613c5fa3ec938e0cb3972113e20f4fde6617c88cc98f7e6ec6001e31b5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n },\n "reverse_sort": true\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step rev\nDEBUG cwltool:workflow_job.py:727 [step rev] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step rev] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step rev] start\nDEBUG cwltool:command_line_tool.py:982 [job rev] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/revtool.cwl as part of step rev\nDEBUG cwltool:command_line_tool.py:988 [job rev] {\n "revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job rev] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job rev] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "revtool_input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "dirname": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job rev] initial work dir {}\nINFO cwltool:job.py:266 [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:job.py:905 [job rev] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 97fe1b50b4582cebc7d853796ebd62e3e163aa3f data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nINFO cwltool:job.py:419 [job rev] completed success\nDEBUG cwltool:job.py:422 [job rev] outputs {\n "revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step rev] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:572 [step rev] completed success\nDEBUG cwltool:job.py:446 [job rev] Removing input staging directory /private/tmp/docker_tmp0onaxo3l\nDEBUG cwltool:job.py:454 [job rev] Removing temporary directory /private/tmp/docker_tmpwl097n7z\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step sorted\nDEBUG cwltool:workflow_job.py:727 [step sorted] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step sorted] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:75 [step sorted] start\nDEBUG cwltool:command_line_tool.py:982 [job sorted] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sorttool.cwl as part of step sorted\nDEBUG cwltool:command_line_tool.py:988 [job sorted] {\n "reverse": true,\n "sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job sorted] path mappings is {\n "file:///private/tmp/docker_tmpo8j3qsh0/output.txt": [\n "/private/tmp/docker_tmpo8j3qsh0/output.txt",\n "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job sorted] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sort"\n },\n {\n "position": [\n 1,\n "reverse"\n ],\n "prefix": "--reverse",\n "datum": true\n },\n {\n "position": [\n 2,\n "sorted_input"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1",\n "path": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "dirname": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job sorted] initial work dir {}\nINFO cwltool:job.py:266 [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\nINFO cwltool:job.py:905 [job sorted] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: b9214658cc453331b62c2282b772a5c063dbd284 data/b9/b9214658cc453331b62c2282b772a5c063dbd284\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nINFO cwltool:job.py:419 [job sorted] completed success\nDEBUG cwltool:job.py:422 [job sorted] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step sorted] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step sorted] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:job.py:446 [job sorted] Removing input staging directory /private/tmp/docker_tmpt9i2u3d_\nDEBUG cwltool:job.py:454 [job sorted] Removing temporary directory /private/tmp/docker_tmp7ypgmrbr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplkmwaaf_/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplkmwaaf_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp46e4pq4y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo8j3qsh0\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: df915edbd6b5e75857277eb6c8e1377f0d051ef1 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4e56225fad8da955eebc34f2c094def00b9a7b6b39c500bd4ba036618c22e6f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 42a067ea2914371f209f8c25161dee0d1589e739c64f3275519f23d0af480afc636ea8b3298663632e89b2033c18a855ad9eb5290298ed00837688a946ac1523 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 553157706bf95e14c524a396a623d0f3f87f8ecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c6eccb1bc96bd4f55d03be6f4c0262a736dd8296ecae60d0d403bc9bfc8ca92b metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: f8c2586c8f0749fe5ef9e772f752c63acc2ba9dc8176e2cd8da9e677b952f7ba5a8410f062937ee19a3db25b2a414ef3566294dec7e6b6d011f21d176f3e4e3f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: ca44d2cee82bdf4159a998516a8b7d97de4becde metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 9abbc3a964398906a0a6c446f05be412b4f818c5df80213eefb95585644407f9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4dd04bc545f060056ec3c0eb38c22e70e30c30f4b3d633c60a802e4fcb4607737e7938f57b1eaea5a7044b23bf39461a15ccd68a344564b0a257cb7c966d8562 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b52bb0536caa8678dee76e093bab66c9f6ab72d8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fe046d6822ede74b785f00faa9e38aeeb92d573926c5e8f0dc3e87ddcf655336 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 3fe06b96dca53c5afed7eee93e58b27dd8330c34ce5436271af797259e4ffbc9790bb32f8cdab7244e1a83d0f8f1137464dc0dd757d841ac69412932cf09a9f9 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e58bcf95cb06e3d42132d9c488c389eb62de0170 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 27f34aff0b66f02249b46599489c42e37efc5de28e05274bba403a11a31bd86e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4f70440a6e4c80363471248e4d36d4df1a61f6bdeebdc41391bab98dcc5715361142776d4dd4dcc2b9f81d4687b83ea3a259c4a52374d0e6bed988bb6cfc8683 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: bb4d8f1c88da465df4d205fe71778cf5ee0c971e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 45e8790efb18825deb4c136d97032976f831b167076b31e43bd6ae66fc7466d7 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: bad9c61094a072702da2befe78c06dc406039eba8d4f5abeb39fb0646589428829d6e32ce91b705be4d0b9eba94cad5ca02e0665a23e9190438ef61b05611244 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'sorted_output\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 0536da382206c737b78578fb4cd56d470854cb65 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: ca8f0addfb91188dc24d6f6f2455b58ba794fa05417a99e239993ca8a25627c4 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 1ecd7b38f4685c4c7c7a124deaf30613ef849999f7aa5afb3b537d294a9e66933052c4e35fcb2d7a37e565e33a918c497349b9fc901cf828c5f9cd592dce1114 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: eac590a030efa84e4abe5c70bfbbe059d59cb909 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c85344af5e84a113da5636b4c42935c478fe1b587b2f84f82aa07465a71ce1d1 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fc05d8795084ee56e93edfd135c625c462e71dfaed99a7dc613264eb2b8a75a518580a187fb580fa9309c4cb1398a6501040c6251a221f31cbe67c5576a5d799 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: a7199d53b1f707ab9bfa7a88f832a843a05da1b5 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 44dad89d06c949f171fb43e2c2a870f92520a7d288460cafadfd19afefb7697c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fed9bf631358efdec9cb96154215b41a76dc6b7cd38eeb794f6a94212e5fcf868dcc776b0cec9d950de8370d3e4399a7c36833da2d5bdebfb0e193d813047ad4 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 825bbdb1ae0c5b4dab6115409f478fd2b7546ef1 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 65c5c5444143e944a90a7ec7fed5e89f3b4195f53a84f0747bca4875ad8602ec bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 9212abe820053e53692266203ba3819ceae75bb7f5d82f74281d7d1e9e0682ee506d9b210ef2d2bae5396e8d0f751bafbdf1f361747bf3cdc4d9aaa247919f25 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance')], 'duration': 0.0007942510001157643, 'start': 1685951458.580619, 'stop': 1685951458.581415, '$report_type': 'TestReport', 'item_index': 525, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_revsort_workflow + location: ('tests/test_provenance.py', 74, 'test_revsort_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + when: runtest + nodeid: tests/test_provenance.py::test_revsort_workflow + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut + location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow_shortcut', 'location': ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut'), 'keywords': {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014417179991141893, 'start': 1685951458.583897, 'stop': 1685951458.5853388, '$report_type': 'TestReport', 'item_index': 526, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u6e2c\\u8a66]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u6e2c\\u8a66]'), 'keywords': {'test_unicode_in_output_files[\\u6e2c\\u8a66]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u6e2c\\u8a66': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/%E6%B8%AC%E8%A9%A6",\n "basename": "測試",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test"\n },\n "output": "\\u6e2c\\u8a66"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u6e2c\\u8a66"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "dirname": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_8] /private/tmp/docker_tmpvb00lkdp$ cat \\\n /private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test > /private/tmp/docker_tmpvb00lkdp/測試\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_8] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvb00lkdp/%E6%B8%AC%E8%A9%A6",\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] Removing input staging directory /private/tmp/docker_tmpj0hp0cs6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] Removing temporary directory /private/tmp/docker_tmpm9tfik8b\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpvb00lkdp/測試 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvb00lkdp\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test"\n },\n "output": "\\u6e2c\\u8a66"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_8] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_8] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u6e2c\\u8a66"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_8] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "dirname": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_8] initial work dir {}\nINFO cwltool:job.py:266 [job script_8] /private/tmp/docker_tmpvb00lkdp$ cat \\\n /private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test > /private/tmp/docker_tmpvb00lkdp/測試\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_8] completed success\nDEBUG cwltool:job.py:422 [job script_8] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvb00lkdp/%E6%B8%AC%E8%A9%A6",\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_8] Removing input staging directory /private/tmp/docker_tmpj0hp0cs6\nDEBUG cwltool:job.py:454 [job script_8] Removing temporary directory /private/tmp/docker_tmpm9tfik8b\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvb00lkdp/測試 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvb00lkdp\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.739881903999958, 'start': 1685951458.314523, 'stop': 1685951459.054388, '$report_type': 'TestReport', 'item_index': 504, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u6e2c\\u8a66]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u6e2c\\u8a66]'), 'keywords': {'test_unicode_in_output_files[\\u6e2c\\u8a66]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u6e2c\\u8a66': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/%E6%B8%AC%E8%A9%A6",\n "basename": "測試",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test"\n },\n "output": "\\u6e2c\\u8a66"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u6e2c\\u8a66"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "dirname": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_8] /private/tmp/docker_tmpvb00lkdp$ cat \\\n /private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test > /private/tmp/docker_tmpvb00lkdp/測試\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_8] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvb00lkdp/%E6%B8%AC%E8%A9%A6",\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] Removing input staging directory /private/tmp/docker_tmpj0hp0cs6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] Removing temporary directory /private/tmp/docker_tmpm9tfik8b\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpvb00lkdp/測試 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvb00lkdp\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test"\n },\n "output": "\\u6e2c\\u8a66"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_8] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_8] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u6e2c\\u8a66"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_8] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "dirname": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_8] initial work dir {}\nINFO cwltool:job.py:266 [job script_8] /private/tmp/docker_tmpvb00lkdp$ cat \\\n /private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test > /private/tmp/docker_tmpvb00lkdp/測試\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_8] completed success\nDEBUG cwltool:job.py:422 [job script_8] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvb00lkdp/%E6%B8%AC%E8%A9%A6",\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_8] Removing input staging directory /private/tmp/docker_tmpj0hp0cs6\nDEBUG cwltool:job.py:454 [job script_8] Removing temporary directory /private/tmp/docker_tmpm9tfik8b\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvb00lkdp/測試 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvb00lkdp\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007373680000455352, 'start': 1685951459.0556428, 'stop': 1685951459.056383, '$report_type': 'TestReport', 'item_index': 504, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u6e2c\u8a66] + location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u6e2c\\u8a66]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_stderr + location: ('tests/test_stdout_stderr_log_dir.py', 43, 'test_log_dir_echo_stderr') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_stderr', 'location': ('tests/test_stdout_stderr_log_dir.py', 43, 'test_log_dir_echo_stderr'), 'keywords': {'test_log_dir_echo_stderr': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018100770003002253, 'start': 1685951459.058351, 'stop': 1685951459.060163, '$report_type': 'TestReport', 'item_index': 597, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_no_output', 'location': ('tests/test_stdout_stderr_log_dir.py', 22, 'test_log_dir_echo_no_output'), 'keywords': {'test_log_dir_echo_no_output': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl",\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo] initializing from file:///Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl#echo\nDEBUG cwltool:command_line_tool.py:988 [job echo] {\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n "inp"\n ],\n "datum": "hello"\n }\n]\nDEBUG cwltool:job.py:215 [job echo] initial work dir {}\nINFO cwltool:job.py:266 [job echo] /private/tmp/docker_tmp0vbn7hgf$ echo \\\n hello > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_log_dir_echo_no_output0/echo/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo] completed success\nDEBUG cwltool:job.py:422 [job echo] outputs {}\nDEBUG cwltool:job.py:446 [job echo] Removing input staging directory /private/tmp/docker_tmpcmod_263\nDEBUG cwltool:job.py:454 [job echo] Removing temporary directory /private/tmp/docker_tmpavw9i6k7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0vbn7hgf\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7119449290003104, 'start': 1685951458.5484328, 'stop': 1685951459.260361, '$report_type': 'TestReport', 'item_index': 596, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_no_output', 'location': ('tests/test_stdout_stderr_log_dir.py', 22, 'test_log_dir_echo_no_output'), 'keywords': {'test_log_dir_echo_no_output': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl",\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo] initializing from file:///Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl#echo\nDEBUG cwltool:command_line_tool.py:988 [job echo] {\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n "inp"\n ],\n "datum": "hello"\n }\n]\nDEBUG cwltool:job.py:215 [job echo] initial work dir {}\nINFO cwltool:job.py:266 [job echo] /private/tmp/docker_tmp0vbn7hgf$ echo \\\n hello > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_log_dir_echo_no_output0/echo/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo] completed success\nDEBUG cwltool:job.py:422 [job echo] outputs {}\nDEBUG cwltool:job.py:446 [job echo] Removing input staging directory /private/tmp/docker_tmpcmod_263\nDEBUG cwltool:job.py:454 [job echo] Removing temporary directory /private/tmp/docker_tmpavw9i6k7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0vbn7hgf\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005319940000845236, 'start': 1685951459.2613251, 'stop': 1685951459.261858, '$report_type': 'TestReport', 'item_index': 596, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_no_output + location: ('tests/test_stdout_stderr_log_dir.py', 22, 'test_log_dir_echo_no_output') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-False-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 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pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_streaming.py::test_input_can_be_named_pipe[False-True-True]', 'location': ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-True-True]'), 'keywords': {'test_input_can_be_named_pipe[False-True-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'False-True-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_2] {\n "inp": {\n "class": "File",\n "location": 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'item_index': 601, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-True-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-True-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-False-True]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> 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pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_streaming.py::test_input_can_be_named_pipe[False-False-True]', 'location': ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-False-True]'), 'keywords': {'test_input_can_be_named_pipe[False-False-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'False-False-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] {\n "inp": {\n "class": "File",\n "location": 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cwltool:command_line_tool.py:982 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\nDEBUG cwltool:command_line_tool.py:988 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "streamable": false,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n 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'item_index': 602, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-False-True] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-False-True]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0]', 'location': ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]'), 'keywords': {'test_subclass_CLT[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006368040003508213, 'start': 1685951459.294997, 'stop': 1685951459.295636, '$report_type': 'TestReport', 'item_index': 603, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0]', 'location': ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]'), 'keywords': {'test_subclass_CLT[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.004742043999613088, 'start': 1685951459.296237, 'stop': 1685951459.300981, '$report_type': 'TestReport', 'item_index': 603, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log_override', 'location': ('tests/test_secrets.py', 101, 'test_secret_workflow_log_override'), 'keywords': {'test_secret_workflow_log_override': 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"Hoopla!"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "pw": "Hoopla!"\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "Hoopla!"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "Hoopla!"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_job.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "pw": "Hoopla!"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {\n "_:efa2380f-a71c-428d-b7d9-1ac6fbb22b99": [\n "username: user\\npassword: Hoopla!\\n",\n "/ZYBRaV/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpdjx8sgdx$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdjx8sgdx,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1pq6g9g1,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2ewi2yx1/20230605095058-275748.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n cat \\\n example.conf > /private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19\nINFO cwltool:job.py:905 [job step1_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpor336_66\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmp1pq6g9g1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmps8bqpoe9/bc8b5192097de6a54afeeb064f187d67a8cfff19\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmxm82p8l\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdjx8sgdx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.7880733340007282, 'start': 1685951457.512193, 'stop': 1685951459.3002229, '$report_type': 'TestReport', 'item_index': 585, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0]', 'location': ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]'), 'keywords': {'test_subclass_CLT[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002549229993746849, 'start': 1685951459.301441, 'stop': 1685951459.301697, '$report_type': 'TestReport', 'item_index': 603, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log_override', 'location': ('tests/test_secrets.py', 101, 'test_secret_workflow_log_override'), 'keywords': {'test_secret_workflow_log_override': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmps8bqpoe9/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "path": "/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmps8bqpoe9/bc8b5192097de6a54afeeb064f187d67a8cfff19"\n }\n}'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl",\n "pw": "Hoopla!"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "pw": "Hoopla!"\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "Hoopla!"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "Hoopla!"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_job.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "pw": "Hoopla!"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {\n "_:efa2380f-a71c-428d-b7d9-1ac6fbb22b99": [\n "username: user\\npassword: Hoopla!\\n",\n "/ZYBRaV/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpdjx8sgdx$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdjx8sgdx,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1pq6g9g1,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2ewi2yx1/20230605095058-275748.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n cat \\\n example.conf > /private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19\nINFO cwltool:job.py:905 [job step1_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpor336_66\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmp1pq6g9g1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmps8bqpoe9/bc8b5192097de6a54afeeb064f187d67a8cfff19\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmxm82p8l\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdjx8sgdx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0004045150008096243, 'start': 1685951459.301536, 'stop': 1685951459.301941, '$report_type': 'TestReport', 'item_index': 585, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_secrets.py::test_secret_workflow_log_override + location: ('tests/test_secrets.py', 101, 'test_secret_workflow_log_override') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1]', 'location': ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]'), 'keywords': {'test_subclass_CLT[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00045941999997012317, 'start': 1685951459.303957, 'stop': 1685951459.3044171, '$report_type': 'TestReport', 'item_index': 604, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity_pullfolder', 'location': ('tests/test_singularity.py', 19, 'test_singularity_pullfolder'), 'keywords': {'test_singularity_pullfolder': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 20, 'Skipped: Requires that version 2.6.x of singularity executable version is on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00024390599992329953, 'start': 1685951459.303614, 'stop': 1685951459.303859, '$report_type': 'TestReport', 'item_index': 586, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity.py::test_singularity_pullfolder + location: ('tests/test_singularity.py', 19, 'test_singularity_pullfolder') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity_pullfolder', 'location': ('tests/test_singularity.py', 19, 'test_singularity_pullfolder'), 'keywords': {'test_singularity_pullfolder': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00027451900041342014, 'start': 1685951459.3052318, 'stop': 1685951459.3055081, '$report_type': 'TestReport', 'item_index': 586, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_singularity.py::test_singularity_pullfolder + location: ('tests/test_singularity.py', 19, 'test_singularity_pullfolder') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity.py::test_singularity_workflow + location: ('tests/test_singularity.py', 44, 'test_singularity_workflow') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity_workflow', 'location': ('tests/test_singularity.py', 44, 'test_singularity_workflow'), 'keywords': {'test_singularity_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 45, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00023849699937272817, 'start': 1685951459.3082922, 'stop': 1685951459.308532, '$report_type': 'TestReport', 'item_index': 587, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity_workflow', 'location': ('tests/test_singularity.py', 44, 'test_singularity_workflow'), 'keywords': {'test_singularity_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00020401000074343756, 'start': 1685951459.3092139, 'stop': 1685951459.30942, '$report_type': 'TestReport', 'item_index': 587, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_singularity.py::test_singularity_workflow + location: ('tests/test_singularity.py', 44, 'test_singularity_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subclass_mypyc.py::test_serialize_builder + location: ('tests/test_subclass_mypyc.py', 43, 'test_serialize_builder') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subclass_mypyc.py::test_serialize_builder', 'location': 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'$report_type': 'TestReport', 'item_index': 605, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subclass_mypyc.py::test_serialize_builder + location: ('tests/test_subclass_mypyc.py', 43, 'test_serialize_builder') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1] + location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_get_subgraph + location: ('tests/test_subgraph.py', 26, 'test_get_subgraph') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_get_subgraph', 'location': 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tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1]', 'location': ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]'), 'keywords': {'test_subclass_exprtool[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 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'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00027535600020200945, 'start': 1685951459.328183, 'stop': 1685951459.328459, '$report_type': 'TestReport', 'item_index': 606, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] + location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints + location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqshints', 'location': ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints'), 'keywords': {'test_single_process_inherit_reqshints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013924539998697583, 'start': 1685951459.329356, 'stop': 1685951459.330749, '$report_type': 'TestReport', 'item_index': 611, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_get_subgraph', 'location': ('tests/test_subgraph.py', 26, 'test_get_subgraph'), 'keywords': {'test_get_subgraph': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1\x1b[0m\n"), ('Captured log call', "WARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.14068840500021906, 'start': 1685951459.316004, 'stop': 1685951459.456691, '$report_type': 'TestReport', 'item_index': 608, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_get_subgraph', 'location': ('tests/test_subgraph.py', 26, 'test_get_subgraph'), 'keywords': {'test_get_subgraph': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1\x1b[0m\n"), ('Captured log call', "WARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.00024345899964828277, 'start': 1685951459.457286, 'stop': 1685951459.45753, '$report_type': 'TestReport', 'item_index': 608, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_get_subgraph + location: ('tests/test_subgraph.py', 26, 'test_get_subgraph') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_get_subgraph_long_out_form + location: ('tests/test_subgraph.py', 55, 'test_get_subgraph_long_out_form') + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_get_subgraph_long_out_form', 'location': ('tests/test_subgraph.py', 55, 'test_get_subgraph_long_out_form'), 'keywords': {'test_get_subgraph_long_out_form': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003143270005239174, 'start': 1685951459.4586198, 'stop': 1685951459.458936, '$report_type': 'TestReport', 'item_index': 609, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] +pif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'te pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_for_910', 'location': ('tests/test_relocate.py', 14, 'test_for_910'), 'keywords': {'test_for_910': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output_folder": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default",\n "basename": "default",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt",\n "basename": "file.txt",\n "checksum": "sha1$7b502c3a1f48c8609ae212cdfb639dee39673f5e",\n "size": 11,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default"\n }\n}{\n "output_folder": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default",\n "basename": "default",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt",\n "basename": "file.txt",\n "checksum": "sha1$7b502c3a1f48c8609ae212cdfb639dee39673f5e",\n "size": 11,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl'\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/ubuntu']\nUsing default tag: latest\nlatest: Pulling from library/ubuntu\nDigest: sha256:ac58ff7fe25edc58bdf0067ca99df00014dbd032e2246d30a722fa348fd799a5\nStatus: Image is up to date for ubuntu:latest\ndocker.io/library/ubuntu:latest\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] /private/tmp/docker_tmp_5jmo05k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_5jmo05k,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpampehdwa,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4rhkd8q4/20230605095056-803929.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\ndefault\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl'\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] /private/tmp/docker_tmpdqmzp90p$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqmzp90p,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp7x3ibbqw,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp9i7465r8/20230605095058-538883.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\ndefault\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job 910.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\nDEBUG cwltool:command_line_tool.py:988 [job 910.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job 910.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job 910.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/ubuntu\']\nDEBUG cwltool:job.py:215 [job 910.cwl] initial work dir {\n "_:3e29ab95-b40b-4874-b53d-3e3a756b4ffc": [\n "_:3e29ab95-b40b-4874-b53d-3e3a756b4ffc",\n "/GbFKKR/default",\n "WritableDirectory",\n true\n ],\n "_:3a6ea71c-e219-453f-ae43-5fcd8b01c76b": [\n "Hello world",\n "/GbFKKR/default/file.txt",\n "CreateWritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 910.cwl] /private/tmp/docker_tmp_5jmo05k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_5jmo05k,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpampehdwa,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4rhkd8q4/20230605095056-803929.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\nINFO cwltool:job.py:905 [job 910.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job 910.cwl] completed success\nDEBUG cwltool:job.py:422 [job 910.cwl] outputs {\n "output_folder": {\n "location": "file:///private/tmp/docker_tmp_5jmo05k/default",\n "basename": "default",\n "nameroot": "default",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job 910.cwl] Removing input staging directory /private/tmp/docker_tmp2fseafki\nDEBUG cwltool:job.py:454 [job 910.cwl] Removing temporary directory /private/tmp/docker_tmpampehdwa\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_5jmo05k/default to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_5jmo05k\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job 910.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\nDEBUG cwltool:command_line_tool.py:988 [job 910.cwl_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job 910.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job 910.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job 910.cwl_2] initial work dir {\n "_:9bd8d9fb-ba21-4479-86cb-92132d242768": [\n "_:9bd8d9fb-ba21-4479-86cb-92132d242768",\n "/GbFKKR/default",\n "WritableDirectory",\n true\n ],\n "_:461b72fd-438a-46ec-9b5f-b069b8590be0": [\n "Hello world",\n "/GbFKKR/default/file.txt",\n "CreateWritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 910.cwl_2] /private/tmp/docker_tmpdqmzp90p$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqmzp90p,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp7x3ibbqw,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp9i7465r8/20230605095058-538883.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\nINFO cwltool:job.py:905 [job 910.cwl_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job 910.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job 910.cwl_2] outputs {\n "output_folder": {\n "location": "file:///private/tmp/docker_tmpdqmzp90p/default",\n "basename": "default",\n "nameroot": "default",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job 910.cwl_2] Removing input staging directory /private/tmp/docker_tmpwt5tsqil\nDEBUG cwltool:job.py:454 [job 910.cwl_2] Removing temporary directory /private/tmp/docker_tmp7x3ibbqw\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdqmzp90p/default to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdqmzp90p/default/file.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdqmzp90p\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 4.948344170000382, 'start': 1685951454.617118, 'stop': 1685951459.5653398, '$report_type': 'TestReport', 'item_index': 574, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_for_910', 'location': ('tests/test_relocate.py', 14, 'test_for_910'), 'keywords': {'test_for_910': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output_folder": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default",\n "basename": "default",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt",\n "basename": "file.txt",\n "checksum": "sha1$7b502c3a1f48c8609ae212cdfb639dee39673f5e",\n "size": 11,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default"\n }\n}{\n "output_folder": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default",\n "basename": "default",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt",\n "basename": "file.txt",\n "checksum": "sha1$7b502c3a1f48c8609ae212cdfb639dee39673f5e",\n "size": 11,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl'\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/ubuntu']\nUsing default tag: latest\nlatest: Pulling from library/ubuntu\nDigest: sha256:ac58ff7fe25edc58bdf0067ca99df00014dbd032e2246d30a722fa348fd799a5\nStatus: Image is up to date for ubuntu:latest\ndocker.io/library/ubuntu:latest\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] /private/tmp/docker_tmp_5jmo05k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_5jmo05k,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpampehdwa,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4rhkd8q4/20230605095056-803929.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\ndefault\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl'\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] /private/tmp/docker_tmpdqmzp90p$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqmzp90p,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp7x3ibbqw,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp9i7465r8/20230605095058-538883.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\ndefault\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job 910.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\nDEBUG cwltool:command_line_tool.py:988 [job 910.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job 910.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job 910.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/ubuntu\']\nDEBUG cwltool:job.py:215 [job 910.cwl] initial work dir {\n "_:3e29ab95-b40b-4874-b53d-3e3a756b4ffc": [\n "_:3e29ab95-b40b-4874-b53d-3e3a756b4ffc",\n "/GbFKKR/default",\n "WritableDirectory",\n true\n ],\n "_:3a6ea71c-e219-453f-ae43-5fcd8b01c76b": [\n "Hello world",\n "/GbFKKR/default/file.txt",\n "CreateWritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 910.cwl] /private/tmp/docker_tmp_5jmo05k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_5jmo05k,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpampehdwa,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4rhkd8q4/20230605095056-803929.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\nINFO cwltool:job.py:905 [job 910.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job 910.cwl] completed success\nDEBUG cwltool:job.py:422 [job 910.cwl] outputs {\n "output_folder": {\n "location": "file:///private/tmp/docker_tmp_5jmo05k/default",\n "basename": "default",\n "nameroot": "default",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job 910.cwl] Removing input staging directory /private/tmp/docker_tmp2fseafki\nDEBUG cwltool:job.py:454 [job 910.cwl] Removing temporary directory /private/tmp/docker_tmpampehdwa\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_5jmo05k/default to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_5jmo05k\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job 910.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\nDEBUG cwltool:command_line_tool.py:988 [job 910.cwl_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job 910.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job 910.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job 910.cwl_2] initial work dir {\n "_:9bd8d9fb-ba21-4479-86cb-92132d242768": [\n "_:9bd8d9fb-ba21-4479-86cb-92132d242768",\n "/GbFKKR/default",\n "WritableDirectory",\n true\n ],\n "_:461b72fd-438a-46ec-9b5f-b069b8590be0": [\n "Hello world",\n "/GbFKKR/default/file.txt",\n "CreateWritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 910.cwl_2] /private/tmp/docker_tmpdqmzp90p$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqmzp90p,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp7x3ibbqw,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp9i7465r8/20230605095058-538883.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\nINFO cwltool:job.py:905 [job 910.cwl_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job 910.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job 910.cwl_2] outputs {\n "output_folder": {\n "location": "file:///private/tmp/docker_tmpdqmzp90p/default",\n "basename": "default",\n "nameroot": "default",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job 910.cwl_2] Removing input staging directory /private/tmp/docker_tmpwt5tsqil\nDEBUG cwltool:job.py:454 [job 910.cwl_2] Removing temporary directory /private/tmp/docker_tmp7x3ibbqw\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdqmzp90p/default to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdqmzp90p/default/file.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdqmzp90p\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008282369999506045, 'start': 1685951459.567082, 'stop': 1685951459.5679119, '$report_type': 'TestReport', 'item_index': 574, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_relocate.py::test_for_910 + location: ('tests/test_relocate.py', 14, 'test_for_910') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_relocate.py::test_for_conflict_file_names + location: ('tests/test_relocate.py', 20, 'test_for_conflict_file_names') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names', 'location': ('tests/test_relocate.py', 20, 'test_for_conflict_file_names'), 'keywords': {'test_for_conflict_file_names': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013990580000609043, 'start': 1685951459.5697222, 'stop': 1685951459.571127, '$report_type': 'TestReport', 'item_index': 575, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print_unicode', 'location': ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode'), 'keywords': {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix rdfs: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n rdfs:label "Sequence file in FASTA format" ;\n rdfs:comment """Input sequence file in FASTA format (not compressed/zipped!).\nCan be an assembled genome (genome mode) or transcriptome (DNA,\ntranscriptome mode), or protein sequences from an annotated gene set\n(proteins mode).\nNB: select just one transcript/protein per gene for your input,\notherwise they will appear as ‘Duplicated’ matches.\n""" ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m /Users/jasperk/gitlab/cwltool/cwltool/__main__.py 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl'\n")], 'duration': 1.9449515790001897, 'start': 1685951457.6899168, 'stop': 1685951459.634825, '$report_type': 'TestReport', 'item_index': 572, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print_unicode', 'location': ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode'), 'keywords': {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix rdfs: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n rdfs:label "Sequence file in FASTA format" ;\n rdfs:comment """Input sequence file in FASTA format (not compressed/zipped!).\nCan be an assembled genome (genome mode) or transcriptome (DNA,\ntranscriptome mode), or protein sequences from an annotated gene set\n(proteins mode).\nNB: select just one transcript/protein per gene for your input,\notherwise they will appear as ‘Duplicated’ matches.\n""" ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m /Users/jasperk/gitlab/cwltool/cwltool/__main__.py 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl'\n")], 'duration': 0.0006568690005224198, 'start': 1685951459.6365361, 'stop': 1685951459.637194, '$report_type': 'TestReport', 'item_index': 572, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_rdfprint.py::test_rdf_print_unicode + location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity.py::test_singularity_iwdr + location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity_iwdr', 'location': ('tests/test_singularity.py', 62, 'test_singularity_iwdr'), 'keywords': {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.002171388000533625, 'start': 1685951459.638792, 'stop': 1685951459.6409652, '$report_type': 'TestReport', 'item_index': 588, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow_shortcut', 'location': ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut'), 'keywords': {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'failed', 'longrepr': {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 46, 'message': "AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))\nassert 1 == 0"}, 'reprtraceback': {'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_revsort_workflow_shortcut(tmp_path: Path) -> None:', ' """Confirm that using \'cwl:tool\' shortcut still snapshots the CWL files."""', '> folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/revsort-job-shortcut.json"),', ' )'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 89, 'message': ''}, 'style': 'long'}}, {'type': 'ReprEntry', 'data': {'lines': [' def cwltool(tmp_path: Path, *args: Any) -> Path:', ' prov_folder = tmp_path / "provenance"', ' prov_folder.mkdir()', ' new_args = ["--provenance", str(prov_folder)]', ' new_args.extend(args)', ' # Run within a temporary directory to not pollute git checkout', ' tmp_dir = tmp_path / "cwltool-run"', ' tmp_dir.mkdir()', ' with working_directory(tmp_dir):', ' status = main(new_args)', '> assert status == 0, f"Failed: cwltool.main({args})"', "E AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))", 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')"), ('args', "('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',)"), ('prov_folder', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')"), ('new_args', "['--provenance', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance', '/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json']"), ('tmp_dir', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 46, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, 'sections': [], 'chain': [({'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_revsort_workflow_shortcut(tmp_path: Path) -> None:', ' """Confirm that using \'cwl:tool\' shortcut still snapshots the CWL files."""', '> folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/revsort-job-shortcut.json"),', ' )'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 89, 'message': ''}, 'style': 'long'}}, {'type': 'ReprEntry', 'data': {'lines': [' def cwltool(tmp_path: Path, *args: Any) -> Path:', ' prov_folder = tmp_path / "provenance"', ' prov_folder.mkdir()', ' new_args = ["--provenance", str(prov_folder)]', ' new_args.extend(args)', ' # Run within a temporary directory to not pollute git checkout', ' tmp_dir = tmp_path / "cwltool-run"', ' tmp_dir.mkdir()', ' with working_directory(tmp_dir):', ' status = main(new_args)', '> assert status == 0, f"Failed: cwltool.main({args})"', "E AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))", 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')"), ('args', "('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',)"), ('prov_folder', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')"), ('new_args', "['--provenance', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance', '/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json']"), ('tmp_dir', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 46, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 46, 'message': "AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))\nassert 1 == 0"}, None)]}, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mERROR\x1b[0m \x1b[31mGot workflow error\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json",\n "reverse_sort": true,\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "@id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'reverse_sort\': True, \'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 5e5a492f53d25bdd4e5e7e3ee61407036d74c263 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 8322e8a8c8231f681484b7cf2caae8110994310a49cbb0679a9dc40993bd863d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 57b1439b4885ea2220eb4b4177e0c82d5724d29dd75ce4ce5b4041c9a9c705cadc478ed732165222d7fff8788ef51dc4c5478ae1586d34fa3bec637b183cdcd6 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nERROR cwltool:executors.py:250 Got workflow error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: d4e780eac6b995170c5544138e51cee42bf82b02 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 71854d40af17ddaad25710ff92bed3033edc5312cea32640d1780241b99df51f metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: ba634748b2a242590fe4f2f293ea32ab4cae028fc7ba9a83b3ce2964374030766b9b71e13fe231a9e27877e79b5c939c949ce2cab6806a002f4ef8005ea34504 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: fa166224b2884b8c1a7019701241269f0fe8f4ba metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: b220ef2e9661453dc089f3645d905eb38ede5f81267288875ebaa393f440a3b6 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 67dc40c370f4eb425ad35887933493d90057b10fb0d6c65a7b9dd47fd482ce515036fe98304f7a6254891a4240f1f515e792dd7c3610f9d4e38c5954de185854 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 7b845a04531a0aea8b66445b3cb5dfd3cc38987e bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 674fc7391ca2a9c892cc4a7b8f6d69ef84f4debea78506708c389a4611090a94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 350e30ea50137627007116ea6a7b9e3f71a7b9e01835e5e0b82201f45bd7f577cc3f294c98401c2afabc72bd7c331d4a7ad8cb70dcac056749b3d897311a5e03 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')], 'duration': 0.9283330289999867, 'start': 1685951458.585697, 'stop': 1685951459.514008, '$report_type': 'TestReport', 'item_index': 526, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow_shortcut', 'location': ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut'), 'keywords': {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mERROR\x1b[0m \x1b[31mGot workflow error\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json",\n "reverse_sort": true,\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "@id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'reverse_sort\': True, \'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 5e5a492f53d25bdd4e5e7e3ee61407036d74c263 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 8322e8a8c8231f681484b7cf2caae8110994310a49cbb0679a9dc40993bd863d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 57b1439b4885ea2220eb4b4177e0c82d5724d29dd75ce4ce5b4041c9a9c705cadc478ed732165222d7fff8788ef51dc4c5478ae1586d34fa3bec637b183cdcd6 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nERROR cwltool:executors.py:250 Got workflow error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: d4e780eac6b995170c5544138e51cee42bf82b02 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 71854d40af17ddaad25710ff92bed3033edc5312cea32640d1780241b99df51f metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: ba634748b2a242590fe4f2f293ea32ab4cae028fc7ba9a83b3ce2964374030766b9b71e13fe231a9e27877e79b5c939c949ce2cab6806a002f4ef8005ea34504 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: fa166224b2884b8c1a7019701241269f0fe8f4ba metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: b220ef2e9661453dc089f3645d905eb38ede5f81267288875ebaa393f440a3b6 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 67dc40c370f4eb425ad35887933493d90057b10fb0d6c65a7b9dd47fd482ce515036fe98304f7a6254891a4240f1f515e792dd7c3610f9d4e38c5954de185854 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 7b845a04531a0aea8b66445b3cb5dfd3cc38987e bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 674fc7391ca2a9c892cc4a7b8f6d69ef84f4debea78506708c389a4611090a94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 350e30ea50137627007116ea6a7b9e3f71a7b9e01835e5e0b82201f45bd7f577cc3f294c98401c2afabc72bd7c331d4a7ad8cb70dcac056749b3d897311a5e03 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')], 'duration': 0.0016798560000097496, 'start': 1685951459.699641, 'stop': 1685951459.701323, '$report_type': 'TestReport', 'item_index': 526, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut + location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_nested_workflow + location: ('tests/test_provenance.py', 98, 'test_nested_workflow') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_nested_workflow', 'location': ('tests/test_provenance.py', 98, 'test_nested_workflow'), 'keywords': {'test_nested_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018565800000942545, 'start': 1685951459.703209, 'stop': 1685951459.705068, '$report_type': 'TestReport', 'item_index': 527, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_stderr', 'location': ('tests/test_stdout_stderr_log_dir.py', 43, 'test_log_dir_echo_stderr'), 'keywords': {'test_log_dir_echo_stderr': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo-stderr.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo-stderr.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo-stderr.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo-stderr.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "echo $(inputs.message) 1>&2"\n }\n]\nDEBUG cwltool:job.py:215 [job echo-stderr.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job echo-stderr.cwl] /private/tmp/docker_tmpy47xscwu$ bash \\\n -c \\\n \'echo hello 1>&2\' 2> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_log_dir_echo_stderr0/echo-stderr.cwl/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo-stderr.cwl] completed success\nDEBUG cwltool:job.py:422 [job echo-stderr.cwl] outputs {\n "out": "hello\\n"\n}\nDEBUG cwltool:job.py:446 [job echo-stderr.cwl] Removing input staging directory /private/tmp/docker_tmpq05r80i_\nDEBUG cwltool:job.py:454 [job echo-stderr.cwl] Removing temporary directory /private/tmp/docker_tmpyd_d2wbt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpy47xscwu\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7239499830002387, 'start': 1685951459.06056, 'stop': 1685951459.7844942, '$report_type': 'TestReport', 'item_index': 597, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_stderr', 'location': ('tests/test_stdout_stderr_log_dir.py', 43, 'test_log_dir_echo_stderr'), 'keywords': {'test_log_dir_echo_stderr': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo-stderr.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo-stderr.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo-stderr.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo-stderr.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "echo $(inputs.message) 1>&2"\n }\n]\nDEBUG cwltool:job.py:215 [job echo-stderr.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job echo-stderr.cwl] /private/tmp/docker_tmpy47xscwu$ bash \\\n -c \\\n \'echo hello 1>&2\' 2> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_log_dir_echo_stderr0/echo-stderr.cwl/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo-stderr.cwl] completed success\nDEBUG cwltool:job.py:422 [job echo-stderr.cwl] outputs {\n "out": "hello\\n"\n}\nDEBUG cwltool:job.py:446 [job echo-stderr.cwl] Removing input staging directory /private/tmp/docker_tmpq05r80i_\nDEBUG cwltool:job.py:454 [job echo-stderr.cwl] Removing temporary directory /private/tmp/docker_tmpyd_d2wbt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpy47xscwu\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005019689997425303, 'start': 1685951459.785346, 'stop': 1685951459.785849, '$report_type': 'TestReport', 'item_index': 597, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_stderr + location: ('tests/test_stdout_stderr_log_dir.py', 43, 'test_log_dir_echo_stderr') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_streaming.py::test_regular_file + location: ('tests/test_streaming.py', 47, 'test_regular_file') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_streaming.py::test_regular_file', 'location': ('tests/test_streaming.py', 47, 'test_regular_file'), 'keywords': {'test_regular_file': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003891579999617534, 'start': 1685951459.7871192, 'stop': 1685951459.78751, '$report_type': 'TestReport', 'item_index': 598, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_streaming.py::test_regular_file', 'location': ('tests/test_streaming.py', 47, 'test_regular_file'), 'keywords': {'test_regular_file': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:10b10210-be50-4068-984c-fae3f949ab6d] initializing from _:10b10210-be50-4068-984c-fae3f949ab6d\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:10b10210-be50-4068-984c-fae3f949ab6d] {\n "inp": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:10b10210-be50-4068-984c-fae3f949ab6d] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/sua2u9lg/stgdfe96b72-1c54-4d8b-b17d-d24e7717d04b/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:10b10210-be50-4068-984c-fae3f949ab6d] command line bindings is []\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:10b10210-be50-4068-984c-fae3f949ab6d] initial work dir {}\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:10b10210-be50-4068-984c-fae3f949ab6d] initializing from _:10b10210-be50-4068-984c-fae3f949ab6d\nDEBUG cwltool:command_line_tool.py:988 [job _:10b10210-be50-4068-984c-fae3f949ab6d] {\n "inp": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job _:10b10210-be50-4068-984c-fae3f949ab6d] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/sua2u9lg/stgdfe96b72-1c54-4d8b-b17d-d24e7717d04b/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job _:10b10210-be50-4068-984c-fae3f949ab6d] command line bindings is []\nDEBUG cwltool:job.py:215 [job _:10b10210-be50-4068-984c-fae3f949ab6d] initial work dir {}')], 'duration': 0.007587575999423279, 'start': 1685951459.78817, 'stop': 1685951459.7957592, '$report_type': 'TestReport', 'item_index': 598, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_streaming.py::test_regular_file', 'location': ('tests/test_streaming.py', 47, 'test_regular_file'), 'keywords': {'test_regular_file': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:10b10210-be50-4068-984c-fae3f949ab6d] initializing from _:10b10210-be50-4068-984c-fae3f949ab6d\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:10b10210-be50-4068-984c-fae3f949ab6d] {\n "inp": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:10b10210-be50-4068-984c-fae3f949ab6d] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/sua2u9lg/stgdfe96b72-1c54-4d8b-b17d-d24e7717d04b/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:10b10210-be50-4068-984c-fae3f949ab6d] command line bindings is []\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:10b10210-be50-4068-984c-fae3f949ab6d] initial work dir {}\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:10b10210-be50-4068-984c-fae3f949ab6d] initializing from _:10b10210-be50-4068-984c-fae3f949ab6d\nDEBUG cwltool:command_line_tool.py:988 [job _:10b10210-be50-4068-984c-fae3f949ab6d] {\n "inp": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job _:10b10210-be50-4068-984c-fae3f949ab6d] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n 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cwltool:command_line_tool.py:1000 [job _:10b10210-be50-4068-984c-fae3f949ab6d_2] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_input_can_be_named_pipe_T0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_input_can_be_named_pipe_T0/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/95gkswk7/stg96a99037-19ed-4fe2-9008-08058d8de109/tmp",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job _:10b10210-be50-4068-984c-fae3f949ab6d_2] command line bindings is []\nDEBUG cwltool:job.py:215 [job _:10b10210-be50-4068-984c-fae3f949ab6d_2] initial work dir {}')], 'duration': 0.009799992999433016, 'start': 1685951459.801187, 'stop': 1685951459.810988, '$report_type': 'TestReport', 'item_index': 599, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + 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<_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-True-False] + location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-True-False]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_collision + location: ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_collision', 'location': ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision'), 'keywords': {'test_single_process_inherit_reqs_collision': 1, 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cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp1rf1mf2r$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp1rf1mf2r/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1rf1mf2r/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmpay9r1t0o\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmptl9zl9t0\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1rf1mf2r/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1rf1mf2r\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.823703552000552, 'start': 1685951459.3311412, 'stop': 1685951460.154825, '$report_type': 'TestReport', 'item_index': 611, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqshints', 'location': ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints'), 'keywords': {'test_single_process_inherit_reqshints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp1rf1mf2r$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp1rf1mf2r/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1rf1mf2r/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmpay9r1t0o\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmptl9zl9t0\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1rf1mf2r/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1rf1mf2r\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000500224999996135, 'start': 1685951460.15571, 'stop': 1685951460.156211, '$report_type': 'TestReport', 'item_index': 611, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints + location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision + location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_hints_collision', 'location': ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision'), 'keywords': {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018444249999447493, 'start': 1685951460.158337, 'stop': 1685951460.160183, '$report_type': 'TestReport', 'item_index': 612, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_get_subgraph_long_out_form', 'location': ('tests/test_subgraph.py', 55, 'test_get_subgraph_long_out_form'), 'keywords': {'test_get_subgraph_long_out_form': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', "WARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?")], 'duration': 0.9022642480003924, 'start': 1685951459.459401, 'stop': 1685951460.361644, '$report_type': 'TestReport', 'item_index': 609, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_get_subgraph_long_out_form', 'location': ('tests/test_subgraph.py', 55, 'test_get_subgraph_long_out_form'), 'keywords': {'test_get_subgraph_long_out_form': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', "WARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?")], 'duration': 0.00020006900012958795, 'start': 1685951460.362091, 'stop': 1685951460.362292, '$report_type': 'TestReport', 'item_index': 609, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_get_subgraph_long_out_form + location: ('tests/test_subgraph.py', 55, 'test_get_subgraph_long_out_form') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_get_step + location: ('tests/test_subgraph.py', 70, 'test_get_step') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_get_step', 'location': ('tests/test_subgraph.py', 70, 'test_get_step'), 'keywords': {'test_get_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003287249992354191, 'start': 1685951460.364289, 'stop': 1685951460.364619, '$report_type': 'TestReport', 'item_index': 610, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity_iwdr', 'location': ('tests/test_singularity.py', 62, 'test_singularity_iwdr'), 'keywords': {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:810 Singularity error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 771, in run\n self.get_from_requirements(\n File "/Users/jasperk/gitlab/cwltool/cwltool/singularity.py", line 292, in get_from_requirements\n raise WorkflowException("singularity executable is not available")\ncwltool.errors.WorkflowException: singularity executable is not available\nERROR cwltool:main.py:1373 Workflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available')], 'duration': 0.7381495270001324, 'start': 1685951459.641752, 'stop': 1685951460.379884, '$report_type': 'TestReport', 'item_index': 588, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity_iwdr', 'location': ('tests/test_singularity.py', 62, 'test_singularity_iwdr'), 'keywords': {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:810 Singularity error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 771, in run\n self.get_from_requirements(\n File "/Users/jasperk/gitlab/cwltool/cwltool/singularity.py", line 292, in get_from_requirements\n raise WorkflowException("singularity executable is not available")\ncwltool.errors.WorkflowException: singularity executable is not available\nERROR cwltool:main.py:1373 Workflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available')], 'duration': 0.00043232999996689614, 'start': 1685951460.380364, 'stop': 1685951460.3807979, '$report_type': 'TestReport', 'item_index': 588, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_singularity.py::test_singularity_iwdr + location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull + location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity_incorrect_image_pull', 'location': ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull'), 'keywords': {'test_singularity_incorrect_image_pull': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 84, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00022189900028024567, 'start': 1685951460.381962, 'stop': 1685951460.382185, '$report_type': 'TestReport', 'item_index': 589, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity_incorrect_image_pull', 'location': ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull'), 'keywords': {'test_singularity_incorrect_image_pull': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00021053000000392785, 'start': 1685951460.382848, 'stop': 1685951460.38306, '$report_type': 'TestReport', 'item_index': 589, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull + location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_singularity.py::test_singularity_local + location: ('tests/test_singularity.py', 98, 'test_singularity_local') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity_local', 'location': ('tests/test_singularity.py', 98, 'test_singularity_local'), 'keywords': {'test_singularity_local': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 99, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002089989993692143, 'start': 1685951460.385066, 'stop': 1685951460.3852758, '$report_type': 'TestReport', 'item_index': 590, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_singularity.py::test_singularity_local', 'location': ('tests/test_singularity.py', 98, 'test_singularity_local'), 'keywords': {'test_singularity_local': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002950230000351439, 'start': 1685951460.38608, 'stop': 1685951460.3863769, '$report_type': 'TestReport', 'item_index': 590, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_singularity.py::test_singularity_local + location: ('tests/test_singularity.py', 98, 'test_singularity_local') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step + location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_packed_subwf_step', 'location': ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step'), 'keywords': {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001556540999445133, 'start': 1685951460.3884459, 'stop': 1685951460.390004, '$report_type': 'TestReport', 'item_index': 618, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_get_step', 'location': ('tests/test_subgraph.py', 70, 'test_get_step'), 'keywords': {'test_get_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:00]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1\x1b[0m\n"), ('Captured log call', "WARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.1355143520004276, 'start': 1685951460.364971, 'stop': 1685951460.500483, '$report_type': 'TestReport', 'item_index': 610, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_get_step', 'location': ('tests/test_subgraph.py', 70, 'test_get_step'), 'keywords': {'test_get_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:00]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1\x1b[0m\n"), ('Captured log call', "WARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.00021679000019503292, 'start': 1685951460.5012228, 'stop': 1685951460.501441, '$report_type': 'TestReport', 'item_index': 610, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_get_step + location: ('tests/test_subgraph.py', 70, 'test_get_step') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_subwf_step + location: ('tests/test_subgraph.py', 188, 'test_single_process_subwf_step') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_step', 'location': ('tests/test_subgraph.py', 188, 'test_single_process_subwf_step'), 'keywords': {'test_single_process_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001321605000157433, 'start': 1685951460.5035431, 'stop': 1685951460.5048661, '$report_type': 'TestReport', 'item_index': 617, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_collision', 'location': ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision'), 'keywords': {'test_single_process_inherit_reqs_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmp6nz6ufny$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp6nz6ufny/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6nz6ufny/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmp4ckaad43\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpzyry0m08\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6nz6ufny/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6nz6ufny\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.843506232999971, 'start': 1685951459.815787, 'stop': 1685951460.659273, '$report_type': 'TestReport', 'item_index': 613, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_collision', 'location': ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision'), 'keywords': {'test_single_process_inherit_reqs_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmp6nz6ufny$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp6nz6ufny/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6nz6ufny/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmp4ckaad43\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpzyry0m08\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6nz6ufny/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6nz6ufny\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006021980007062666, 'start': 1685951460.660255, 'stop': 1685951460.6608582, '$report_type': 'TestReport', 'item_index': 613, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_collision + location: ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision + location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision', 'location': ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision'), 'keywords': {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014790080003876938, 'start': 1685951460.662613, 'stop': 1685951460.664093, '$report_type': 'TestReport', 'item_index': 614, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_hints_collision', 'location': ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision'), 'keywords': {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl_2] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl_2] /private/tmp/docker_tmp0rf0qbvp$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp0rf0qbvp/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp0rf0qbvp/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl_2] Removing input staging directory /private/tmp/docker_tmpun5mynhb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl_2] Removing temporary directory /private/tmp/docker_tmp2g3z32z6\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0rf0qbvp/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0rf0qbvp\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9018843539997761, 'start': 1685951460.1607418, 'stop': 1685951461.062607, '$report_type': 'TestReport', 'item_index': 612, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_hints_collision', 'location': ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision'), 'keywords': {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl_2] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl_2] /private/tmp/docker_tmp0rf0qbvp$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp0rf0qbvp/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp0rf0qbvp/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl_2] Removing input staging directory /private/tmp/docker_tmpun5mynhb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl_2] Removing temporary directory /private/tmp/docker_tmp2g3z32z6\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0rf0qbvp/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0rf0qbvp\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007875250003053225, 'start': 1685951461.064188, 'stop': 1685951461.064978, '$report_type': 'TestReport', 'item_index': 612, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision + location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision + location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision', 'location': ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision'), 'keywords': {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0019690780000019004, 'start': 1685951461.066408, 'stop': 1685951461.068379, '$report_type': 'TestReport', 'item_index': 615, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names', 'location': ('tests/test_relocate.py', 20, 'test_for_conflict_file_names'), 'keywords': {'test_for_conflict_file_names': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] inputs {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step step1_5\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_5] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_6] /private/tmp/docker_tmp0419t2y2$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] Removing input staging directory /private/tmp/docker_tmpgggel8mc\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] Removing temporary directory /private/tmp/docker_tmpftf5rp4l\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step step2_4\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_4] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_4\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2] /private/tmp/docker_tmpbg5nbyyo$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] Removing input staging directory /private/tmp/docker_tmph0b3hrp3\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] Removing temporary directory /private/tmp/docker_tmpmhnabfu2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp0419t2y2/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpbg5nbyyo/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp7qi3ddmh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpbg5nbyyo\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp0419t2y2\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step step1_5\nDEBUG cwltool:workflow_job.py:727 [step step1_5] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1_5] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_5\nDEBUG cwltool:command_line_tool.py:988 [job step1_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_6] initial work dir {}\nINFO cwltool:job.py:266 [job step1_6] /private/tmp/docker_tmp0419t2y2$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_6] completed success\nDEBUG cwltool:job.py:422 [job step1_6] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_5] completed success\nDEBUG cwltool:job.py:446 [job step1_6] Removing input staging directory /private/tmp/docker_tmpgggel8mc\nDEBUG cwltool:job.py:454 [job step1_6] Removing temporary directory /private/tmp/docker_tmpftf5rp4l\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step step2_4\nDEBUG cwltool:workflow_job.py:727 [step step2_4] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step2_4] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step2_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_4\nDEBUG cwltool:command_line_tool.py:988 [job step2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step2] initial work dir {}\nINFO cwltool:job.py:266 [job step2] /private/tmp/docker_tmpbg5nbyyo$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step2] completed success\nDEBUG cwltool:job.py:422 [job step2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _7] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step2] Removing input staging directory /private/tmp/docker_tmph0b3hrp3\nDEBUG cwltool:job.py:454 [job step2] Removing temporary directory /private/tmp/docker_tmpmhnabfu2\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0419t2y2/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpbg5nbyyo/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7qi3ddmh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbg5nbyyo\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0419t2y2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.7811133960003644, 'start': 1685951459.571585, 'stop': 1685951461.352656, '$report_type': 'TestReport', 'item_index': 575, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names', 'location': ('tests/test_relocate.py', 20, 'test_for_conflict_file_names'), 'keywords': {'test_for_conflict_file_names': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] inputs {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step step1_5\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_5] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_6] /private/tmp/docker_tmp0419t2y2$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] Removing input staging directory /private/tmp/docker_tmpgggel8mc\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] Removing temporary directory /private/tmp/docker_tmpftf5rp4l\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step step2_4\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_4] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_4\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2] /private/tmp/docker_tmpbg5nbyyo$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] Removing input staging directory /private/tmp/docker_tmph0b3hrp3\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] Removing temporary directory /private/tmp/docker_tmpmhnabfu2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp0419t2y2/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpbg5nbyyo/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp7qi3ddmh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpbg5nbyyo\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp0419t2y2\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step step1_5\nDEBUG cwltool:workflow_job.py:727 [step step1_5] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1_5] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_5\nDEBUG cwltool:command_line_tool.py:988 [job step1_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_6] initial work dir {}\nINFO cwltool:job.py:266 [job step1_6] /private/tmp/docker_tmp0419t2y2$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_6] completed success\nDEBUG cwltool:job.py:422 [job step1_6] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_5] completed success\nDEBUG cwltool:job.py:446 [job step1_6] Removing input staging directory /private/tmp/docker_tmpgggel8mc\nDEBUG cwltool:job.py:454 [job step1_6] Removing temporary directory /private/tmp/docker_tmpftf5rp4l\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step step2_4\nDEBUG cwltool:workflow_job.py:727 [step step2_4] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step2_4] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step2_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_4\nDEBUG cwltool:command_line_tool.py:988 [job step2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step2] initial work dir {}\nINFO cwltool:job.py:266 [job step2] /private/tmp/docker_tmpbg5nbyyo$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step2] completed success\nDEBUG cwltool:job.py:422 [job step2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _7] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step2] Removing input staging directory /private/tmp/docker_tmph0b3hrp3\nDEBUG cwltool:job.py:454 [job step2] Removing temporary directory /private/tmp/docker_tmpmhnabfu2\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0419t2y2/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpbg5nbyyo/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7qi3ddmh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbg5nbyyo\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0419t2y2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0011240349995205179, 'start': 1685951461.354667, 'stop': 1685951461.355793, '$report_type': 'TestReport', 'item_index': 575, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_relocate.py::test_for_conflict_file_names + location: ('tests/test_relocate.py', 20, 'test_for_conflict_file_names') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_relocate.py::test_for_conflict_file_names_nodocker + location: ('tests/test_relocate.py', 39, 'test_for_conflict_file_names_nodocker') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names_nodocker', 'location': ('tests/test_relocate.py', 39, 'test_for_conflict_file_names_nodocker'), 'keywords': {'test_for_conflict_file_names_nodocker': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.002268951000587549, 'start': 1685951461.3601532, 'stop': 1685951461.3624241, '$report_type': 'TestReport', 'item_index': 576, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_packed_subwf_step', 'location': ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step'), 'keywords': {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp65j863ig$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp65j863ig/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp65j863ig/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmp11jtljvb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpwn42k8_w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp65j863ig/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp65j863ig\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1143909949996669, 'start': 1685951460.390568, 'stop': 1685951461.5049338, '$report_type': 'TestReport', 'item_index': 618, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_packed_subwf_step', 'location': ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step'), 'keywords': {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp65j863ig$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp65j863ig/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp65j863ig/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmp11jtljvb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpwn42k8_w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp65j863ig/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp65j863ig\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006726860001435853, 'start': 1685951461.506804, 'stop': 1685951461.507478, '$report_type': 'TestReport', 'item_index': 618, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step + location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step + location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step', 'location': ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step'), 'keywords': {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0021509959997274564, 'start': 1685951461.510327, 'stop': 1685951461.512479, '$report_type': 'TestReport', 'item_index': 619, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_step', 'location': ('tests/test_subgraph.py', 188, 'test_single_process_subwf_step'), 'keywords': {'test_single_process_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmpv_7ba0am$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpv_7ba0am/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpv_7ba0am/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmprro2yksj\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpxjj4rbu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpv_7ba0am/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_single_process_subwf_step0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpv_7ba0am\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.123654173000432, 'start': 1685951460.505218, 'stop': 1685951461.628845, '$report_type': 'TestReport', 'item_index': 617, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_step', 'location': ('tests/test_subgraph.py', 188, 'test_single_process_subwf_step'), 'keywords': {'test_single_process_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmpv_7ba0am$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpv_7ba0am/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpv_7ba0am/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmprro2yksj\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpxjj4rbu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpv_7ba0am/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_single_process_subwf_step0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpv_7ba0am\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008459549999315641, 'start': 1685951461.630202, 'stop': 1685951461.6310499, '$report_type': 'TestReport', 'item_index': 617, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_subwf_step + location: ('tests/test_subgraph.py', 188, 'test_single_process_subwf_step') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_step_subwf_step + location: ('tests/test_subgraph.py', 239, 'test_single_step_subwf_step') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_step_subwf_step', 'location': ('tests/test_subgraph.py', 239, 'test_single_step_subwf_step'), 'keywords': {'test_single_step_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0019193019998056116, 'start': 1685951461.6342149, 'stop': 1685951461.636136, '$report_type': 'TestReport', 'item_index': 620, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision', 'location': ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision'), 'keywords': {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initializing from _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c\nDEBUG cwltool:command_line_tool.py:988 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "valueFrom": "$(runtime.cores)"\n }\n]\nDEBUG cwltool:job.py:215 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initial work dir {}\nINFO cwltool:job.py:266 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] /private/tmp/docker_tmp0kfy0hx0$ echo \\\n 1 > /private/tmp/docker_tmp0kfy0hx0/cores.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] completed success\nDEBUG cwltool:job.py:422 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp0kfy0hx0/cores.txt",\n "basename": "cores.txt",\n "nameroot": "cores",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing input staging directory /private/tmp/docker_tmpy2q4uxic\nDEBUG cwltool:job.py:454 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing temporary directory /private/tmp/docker_tmp3u7l8gu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0kfy0hx0/cores.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1/cores.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0kfy0hx0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0293492290002177, 'start': 1685951460.664522, 'stop': 1685951461.693847, '$report_type': 'TestReport', 'item_index': 614, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision', 'location': ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision'), 'keywords': {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initializing from _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c\nDEBUG cwltool:command_line_tool.py:988 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "valueFrom": "$(runtime.cores)"\n }\n]\nDEBUG cwltool:job.py:215 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initial work dir {}\nINFO cwltool:job.py:266 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] /private/tmp/docker_tmp0kfy0hx0$ echo \\\n 1 > /private/tmp/docker_tmp0kfy0hx0/cores.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] completed success\nDEBUG cwltool:job.py:422 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp0kfy0hx0/cores.txt",\n "basename": "cores.txt",\n "nameroot": "cores",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing input staging directory /private/tmp/docker_tmpy2q4uxic\nDEBUG cwltool:job.py:454 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing temporary directory /private/tmp/docker_tmp3u7l8gu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0kfy0hx0/cores.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1/cores.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0kfy0hx0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005337309994501993, 'start': 1685951461.694844, 'stop': 1685951461.69538, '$report_type': 'TestReport', 'item_index': 614, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision + location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out + location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_step_wfstep_long_out', 'location': ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out'), 'keywords': {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0026018169992312323, 'start': 1685951461.6975958, 'stop': 1685951461.7001998, '$report_type': 'TestReport', 'item_index': 621, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision', 'location': ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision'), 'keywords': {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmpug5wf1yr$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpug5wf1yr/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpug5wf1yr/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmpr2_osg12\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpdzs6emmt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpug5wf1yr/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpug5wf1yr\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0924644189999526, 'start': 1685951461.068767, 'stop': 1685951462.161207, '$report_type': 'TestReport', 'item_index': 615, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision', 'location': ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision'), 'keywords': {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmpug5wf1yr$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpug5wf1yr/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpug5wf1yr/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmpr2_osg12\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpdzs6emmt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpug5wf1yr/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpug5wf1yr\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.001123591000578017, 'start': 1685951462.162127, 'stop': 1685951462.163251, '$report_type': 'TestReport', 'item_index': 615, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision + location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints + location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_only_hints', 'location': ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints'), 'keywords': {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001528846999462985, 'start': 1685951462.165597, 'stop': 1685951462.1671271, '$report_type': 'TestReport', 'item_index': 616, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_step_subwf_step', 'location': ('tests/test_subgraph.py', 239, 'test_single_step_subwf_step'), 'keywords': {'test_single_step_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _21] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\nINFO cwltool:workflow_job.py:765 [workflow _21] start\nDEBUG cwltool:workflow_job.py:777 [workflow _21] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _21] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpxgr4sqjt$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpxgr4sqjt/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _21] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _21] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpb9c06wtf\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7_g0pfz8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpxgr4sqjt/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_single_step_subwf_step0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvvs07dnp\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxgr4sqjt\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9564511730004597, 'start': 1685951461.6367, 'stop': 1685951462.593131, '$report_type': 'TestReport', 'item_index': 620, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_step_subwf_step', 'location': ('tests/test_subgraph.py', 239, 'test_single_step_subwf_step'), 'keywords': {'test_single_step_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _21] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\nINFO cwltool:workflow_job.py:765 [workflow _21] start\nDEBUG cwltool:workflow_job.py:777 [workflow _21] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _21] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpxgr4sqjt$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpxgr4sqjt/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _21] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _21] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpb9c06wtf\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7_g0pfz8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpxgr4sqjt/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_single_step_subwf_step0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvvs07dnp\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxgr4sqjt\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007508689996029716, 'start': 1685951462.5947719, 'stop': 1685951462.595524, '$report_type': 'TestReport', 'item_index': 620, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_step_subwf_step + location: ('tests/test_subgraph.py', 239, 'test_single_step_subwf_step') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_step + location: ('tests/test_subgraph.py', 301, 'test_print_targets_embedded_step') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_print_targets_embedded_step', 'location': ('tests/test_subgraph.py', 301, 'test_print_targets_embedded_step'), 'keywords': {'test_print_targets_embedded_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003762910000659758, 'start': 1685951462.598204, 'stop': 1685951462.598583, '$report_type': 'TestReport', 'item_index': 624, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_step_wfstep_long_out', 'location': ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out'), 'keywords': {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmp_d17nob5$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp_d17nob5/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfmqmaczt\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7l3r954g\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_d17nob5/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnx7s_q9a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_d17nob5\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0173719809999966, 'start': 1685951461.700803, 'stop': 1685951462.7181509, '$report_type': 'TestReport', 'item_index': 621, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_step_wfstep_long_out', 'location': ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out'), 'keywords': {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmp_d17nob5$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp_d17nob5/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfmqmaczt\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7l3r954g\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_d17nob5/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnx7s_q9a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_d17nob5\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00103417099944636, 'start': 1685951462.723277, 'stop': 1685951462.7243142, '$report_type': 'TestReport', 'item_index': 621, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out + location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit + location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_print_targets_embedded_reqsinherit', 'location': ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit'), 'keywords': {'test_print_targets_embedded_reqsinherit': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00034795999999914784, 'start': 1685951462.72735, 'stop': 1685951462.727699, '$report_type': 'TestReport', 'item_index': 625, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_only_hints', 'location': ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints'), 'keywords': {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_no_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_no_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_no_env.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_no_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_no_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_no_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_no_env.cwl] /private/tmp/docker_tmpvp0cy1ef$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpvp0cy1ef/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_no_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_no_env.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpvp0cy1ef/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$ab5f2a9add5f54622dde555ac8ae9a3000e5ee0a",\n "size": 26,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_no_env.cwl] Removing input staging directory /private/tmp/docker_tmp3ef9ddmc\nDEBUG cwltool:job.py:454 [job env-tool2_no_env.cwl] Removing temporary directory /private/tmp/docker_tmp8ts5h8fu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvp0cy1ef/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvp0cy1ef\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9118393700000524, 'start': 1685951462.167519, 'stop': 1685951463.079338, '$report_type': 'TestReport', 'item_index': 616, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_only_hints', 'location': ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints'), 'keywords': {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_no_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_no_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_no_env.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_no_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_no_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_no_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_no_env.cwl] /private/tmp/docker_tmpvp0cy1ef$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpvp0cy1ef/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_no_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_no_env.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpvp0cy1ef/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$ab5f2a9add5f54622dde555ac8ae9a3000e5ee0a",\n "size": 26,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_no_env.cwl] Removing input staging directory /private/tmp/docker_tmp3ef9ddmc\nDEBUG cwltool:job.py:454 [job env-tool2_no_env.cwl] Removing temporary directory /private/tmp/docker_tmp8ts5h8fu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvp0cy1ef/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvp0cy1ef\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006480779993580654, 'start': 1685951463.08046, 'stop': 1685951463.08111, '$report_type': 'TestReport', 'item_index': 616, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints + location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs + location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs', 'location': ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs'), 'keywords': {'test_print_targets_embedded_sub_subwfs': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003258949991504778, 'start': 1685951463.0834339, 'stop': 1685951463.083762, '$report_type': 'TestReport', 'item_index': 626, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names_nodocker', 'location': ('tests/test_relocate.py', 39, 'test_for_conflict_file_names_nodocker'), 'keywords': {'test_for_conflict_file_names_nodocker': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] inputs {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step step2_5\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_5] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2_2] /private/tmp/docker_tmpcelhvc2f$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] Removing input staging directory /private/tmp/docker_tmpb4fzhykd\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] Removing temporary directory /private/tmp/docker_tmpvx5y2bc8\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step step1_6\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_6] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_7] /private/tmp/docker_tmpsy87u4a4$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _8] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] Removing input staging directory /private/tmp/docker_tmpbe_5fs0a\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] Removing temporary directory /private/tmp/docker_tmpv42ahjpr\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpsy87u4a4/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpcelhvc2f/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpeqv1tcya\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpsy87u4a4\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpcelhvc2f\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _8] start\nDEBUG cwltool:workflow_job.py:777 [workflow _8] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step step2_5\nDEBUG cwltool:workflow_job.py:727 [step step2_5] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step2_5] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step2_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_5\nDEBUG cwltool:command_line_tool.py:988 [job step2_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step2_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step2_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step2_2] initial work dir {}\nINFO cwltool:job.py:266 [job step2_2] /private/tmp/docker_tmpcelhvc2f$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step2_2] completed success\nDEBUG cwltool:job.py:422 [job step2_2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2_5] completed success\nDEBUG cwltool:job.py:446 [job step2_2] Removing input staging directory /private/tmp/docker_tmpb4fzhykd\nDEBUG cwltool:job.py:454 [job step2_2] Removing temporary directory /private/tmp/docker_tmpvx5y2bc8\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step step1_6\nDEBUG cwltool:workflow_job.py:727 [step step1_6] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1_6] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1_6] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_6\nDEBUG cwltool:command_line_tool.py:988 [job step1_7] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_7] initial work dir {}\nINFO cwltool:job.py:266 [job step1_7] /private/tmp/docker_tmpsy87u4a4$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_7] completed success\nDEBUG cwltool:job.py:422 [job step1_7] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow _8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _8] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_7] Removing input staging directory /private/tmp/docker_tmpbe_5fs0a\nDEBUG cwltool:job.py:454 [job step1_7] Removing temporary directory /private/tmp/docker_tmpv42ahjpr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpsy87u4a4/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpcelhvc2f/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpeqv1tcya\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsy87u4a4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcelhvc2f\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.8410316479994435, 'start': 1685951461.363033, 'stop': 1685951463.20402, '$report_type': 'TestReport', 'item_index': 576, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names_nodocker', 'location': ('tests/test_relocate.py', 39, 'test_for_conflict_file_names_nodocker'), 'keywords': {'test_for_conflict_file_names_nodocker': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] inputs {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step step2_5\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_5] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2_2] /private/tmp/docker_tmpcelhvc2f$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] Removing input staging directory /private/tmp/docker_tmpb4fzhykd\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] Removing temporary directory /private/tmp/docker_tmpvx5y2bc8\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step step1_6\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_6] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_7] /private/tmp/docker_tmpsy87u4a4$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _8] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] Removing input staging directory /private/tmp/docker_tmpbe_5fs0a\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] Removing temporary directory /private/tmp/docker_tmpv42ahjpr\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpsy87u4a4/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpcelhvc2f/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpeqv1tcya\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpsy87u4a4\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpcelhvc2f\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _8] start\nDEBUG cwltool:workflow_job.py:777 [workflow _8] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step step2_5\nDEBUG cwltool:workflow_job.py:727 [step step2_5] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step2_5] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step2_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_5\nDEBUG cwltool:command_line_tool.py:988 [job step2_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step2_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step2_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step2_2] initial work dir {}\nINFO cwltool:job.py:266 [job step2_2] /private/tmp/docker_tmpcelhvc2f$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step2_2] completed success\nDEBUG cwltool:job.py:422 [job step2_2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2_5] completed success\nDEBUG cwltool:job.py:446 [job step2_2] Removing input staging directory /private/tmp/docker_tmpb4fzhykd\nDEBUG cwltool:job.py:454 [job step2_2] Removing temporary directory /private/tmp/docker_tmpvx5y2bc8\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step step1_6\nDEBUG cwltool:workflow_job.py:727 [step step1_6] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1_6] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1_6] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_6\nDEBUG cwltool:command_line_tool.py:988 [job step1_7] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_7] initial work dir {}\nINFO cwltool:job.py:266 [job step1_7] /private/tmp/docker_tmpsy87u4a4$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_7] completed success\nDEBUG cwltool:job.py:422 [job step1_7] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow _8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _8] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_7] Removing input staging directory /private/tmp/docker_tmpbe_5fs0a\nDEBUG cwltool:job.py:454 [job step1_7] Removing temporary directory /private/tmp/docker_tmpv42ahjpr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpsy87u4a4/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpcelhvc2f/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpeqv1tcya\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsy87u4a4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcelhvc2f\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008877540003595641, 'start': 1685951463.20895, 'stop': 1685951463.20984, '$report_type': 'TestReport', 'item_index': 576, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_relocate.py::test_for_conflict_file_names_nodocker + location: ('tests/test_relocate.py', 39, 'test_for_conflict_file_names_nodocker') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_step_packed_subwf_step + location: ('tests/test_subgraph.py', 271, 'test_single_step_packed_subwf_step') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_step_packed_subwf_step', 'location': ('tests/test_subgraph.py', 271, 'test_single_step_packed_subwf_step'), 'keywords': {'test_single_step_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015094909995241323, 'start': 1685951463.213248, 'stop': 1685951463.2147589, '$report_type': 'TestReport', 'item_index': 622, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_print_targets_embedded_step', 'location': ('tests/test_subgraph.py', 301, 'test_print_targets_embedded_step'), 'keywords': {'test_print_targets_embedded_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/timelimit2-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/timelimit2-wf.cwl'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:924 Input targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 step1 Output targets:\nINFO cwltool:main.py:924 step1 Input targets:\nINFO cwltool:main.py:924 step2 Output targets:\nINFO cwltool:main.py:924 step2 Input targets:")], 'duration': 0.8990280979996896, 'start': 1685951462.599144, 'stop': 1685951463.4981508, '$report_type': 'TestReport', 'item_index': 624, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_print_targets_embedded_step', 'location': ('tests/test_subgraph.py', 301, 'test_print_targets_embedded_step'), 'keywords': {'test_print_targets_embedded_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/timelimit2-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/timelimit2-wf.cwl'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:924 Input targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 step1 Output targets:\nINFO cwltool:main.py:924 step1 Input targets:\nINFO cwltool:main.py:924 step2 Output targets:\nINFO cwltool:main.py:924 step2 Input targets:")], 'duration': 0.00032098200063046534, 'start': 1685951463.498822, 'stop': 1685951463.4991438, '$report_type': 'TestReport', 'item_index': 624, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_step + location: ('tests/test_subgraph.py', 301, 'test_print_targets_embedded_step') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_target.py::test_target + location: ('tests/test_target.py', 5, 'test_target') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_target.py::test_target', 'location': ('tests/test_target.py', 5, 'test_target'), 'keywords': {'test_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002446250000502914, 'start': 1685951463.50105, 'stop': 1685951463.501296, '$report_type': 'TestReport', 'item_index': 627, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step', 'location': ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step'), 'keywords': {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\'\nDEBUG cwltool:command_line_tool.py:982 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json#count-lines17-wf/step1/run/count-lines17-wf.cwl@step_step1@run/stepX/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run/stepY/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run\nDEBUG cwltool:command_line_tool.py:988 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initial work dir {}\nINFO cwltool:job.py:266 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] /private/tmp/docker_tmp_9yt0z8_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_9yt0z8_,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmprz9dykzk,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpsbmfwops/20230605095102-600646.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt > /private/tmp/docker_tmp_9yt0z8_/output\nINFO cwltool:job.py:905 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] completed success\nDEBUG cwltool:job.py:422 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_9yt0z8_/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing input staging directory /private/tmp/docker_tmp89udep8a\nDEBUG cwltool:job.py:454 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing temporary directory /private/tmp/docker_tmprz9dykzk\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_9yt0z8_/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_9yt0z8_\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.11600468800043, 'start': 1685951461.5130591, 'stop': 1685951463.6290119, '$report_type': 'TestReport', 'item_index': 619, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step', 'location': ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step'), 'keywords': {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\'\nDEBUG cwltool:command_line_tool.py:982 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json#count-lines17-wf/step1/run/count-lines17-wf.cwl@step_step1@run/stepX/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run/stepY/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run\nDEBUG cwltool:command_line_tool.py:988 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initial work dir {}\nINFO cwltool:job.py:266 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] /private/tmp/docker_tmp_9yt0z8_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_9yt0z8_,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmprz9dykzk,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpsbmfwops/20230605095102-600646.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt > /private/tmp/docker_tmp_9yt0z8_/output\nINFO cwltool:job.py:905 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] completed success\nDEBUG cwltool:job.py:422 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_9yt0z8_/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing input staging directory /private/tmp/docker_tmp89udep8a\nDEBUG cwltool:job.py:454 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing temporary directory /private/tmp/docker_tmprz9dykzk\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_9yt0z8_/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_9yt0z8_\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008782109998719534, 'start': 1685951463.630854, 'stop': 1685951463.6317341, '$report_type': 'TestReport', 'item_index': 619, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step + location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value + location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_with_step_level_default_value', 'location': ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value'), 'keywords': {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00043156799983989913, 'start': 1685951463.634976, 'stop': 1685951463.6354098, '$report_type': 'TestReport', 'item_index': 623, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_step_packed_subwf_step', 'location': ('tests/test_subgraph.py', 271, 'test_single_step_packed_subwf_step'), 'keywords': {'test_single_step_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "tests/subgraph/env-wf2_subwf-packed.cwl:71:29: object id 'tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in' previously defined\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nWARNING salad:ref_resolver.py:1130 tests/subgraph/env-wf2_subwf-packed.cwl:71:29: object id \'tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step step1_7\nDEBUG cwltool:workflow_job.py:727 [step step1_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_7] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl as part of step step1_7\nDEBUG cwltool:command_line_tool.py:988 [job step1_8] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_8] initial work dir {}\nINFO cwltool:job.py:266 [job step1_8] /private/tmp/docker_tmp6xo49icl$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp6xo49icl/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_8] completed success\nDEBUG cwltool:job.py:422 [job step1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow _9] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_8] Removing input staging directory /private/tmp/docker_tmp9x013gp5\nDEBUG cwltool:job.py:454 [job step1_8] Removing temporary directory /private/tmp/docker_tmpga8veylr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6xo49icl/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_single_step_packed_subwf_0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6xo49icl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp12rf8g5q\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0249070469999424, 'start': 1685951463.215264, 'stop': 1685951464.240148, '$report_type': 'TestReport', 'item_index': 622, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_step_packed_subwf_step', 'location': ('tests/test_subgraph.py', 271, 'test_single_step_packed_subwf_step'), 'keywords': {'test_single_step_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "tests/subgraph/env-wf2_subwf-packed.cwl:71:29: object id 'tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in' previously defined\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nWARNING salad:ref_resolver.py:1130 tests/subgraph/env-wf2_subwf-packed.cwl:71:29: object id \'tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step step1_7\nDEBUG cwltool:workflow_job.py:727 [step step1_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_7] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl as part of step step1_7\nDEBUG cwltool:command_line_tool.py:988 [job step1_8] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_8] initial work dir {}\nINFO cwltool:job.py:266 [job step1_8] /private/tmp/docker_tmp6xo49icl$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp6xo49icl/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_8] completed success\nDEBUG cwltool:job.py:422 [job step1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow _9] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_8] Removing input staging directory /private/tmp/docker_tmp9x013gp5\nDEBUG cwltool:job.py:454 [job step1_8] Removing temporary directory /private/tmp/docker_tmpga8veylr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6xo49icl/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_single_step_packed_subwf_0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6xo49icl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp12rf8g5q\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007419650000883848, 'start': 1685951464.2413802, 'stop': 1685951464.242124, '$report_type': 'TestReport', 'item_index': 622, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_step_packed_subwf_step + location: ('tests/test_subgraph.py', 271, 'test_single_step_packed_subwf_step') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_tmpdir.py::test_docker_commandLineTool_job_tmpdir_prefix + location: ('tests/test_tmpdir.py', 26, 'test_docker_commandLineTool_job_tmpdir_prefix') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_docker_commandLineTool_job_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 26, 'test_docker_commandLineTool_job_tmpdir_prefix'), 'keywords': {'test_docker_commandLineTool_job_tmpdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018374299997958587, 'start': 1685951464.2446148, 'stop': 1685951464.246454, '$report_type': 'TestReport', 'item_index': 630, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_docker_commandLineTool_job_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 26, 'test_docker_commandLineTool_job_tmpdir_prefix'), 'keywords': {'test_docker_commandLineTool_job_tmpdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:51:04]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:654967f3-fadf-4ec8-acdb-74060e241e57] initializing from _:654967f3-fadf-4ec8-acdb-74060e241e57\x1b[0m\n\x1b[32m[2023-06-05 09:51:04]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:654967f3-fadf-4ec8-acdb-74060e241e57] {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:04]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:654967f3-fadf-4ec8-acdb-74060e241e57] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:04]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:654967f3-fadf-4ec8-acdb-74060e241e57] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:654967f3-fadf-4ec8-acdb-74060e241e57] initializing from _:654967f3-fadf-4ec8-acdb-74060e241e57\nDEBUG cwltool:command_line_tool.py:988 [job _:654967f3-fadf-4ec8-acdb-74060e241e57] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:654967f3-fadf-4ec8-acdb-74060e241e57] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:654967f3-fadf-4ec8-acdb-74060e241e57] command line bindings is []')], 'duration': 0.008833896999931312, 'start': 1685951464.247095, 'stop': 1685951464.2559302, '$report_type': 'TestReport', 'item_index': 630, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_docker_commandLineTool_job_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 26, 'test_docker_commandLineTool_job_tmpdir_prefix'), 'keywords': {'test_docker_commandLineTool_job_tmpdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:51:04]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:654967f3-fadf-4ec8-acdb-74060e241e57] initializing from _:654967f3-fadf-4ec8-acdb-74060e241e57\x1b[0m\n\x1b[32m[2023-06-05 09:51:04]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:654967f3-fadf-4ec8-acdb-74060e241e57] {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:04]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:654967f3-fadf-4ec8-acdb-74060e241e57] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:04]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:654967f3-fadf-4ec8-acdb-74060e241e57] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:654967f3-fadf-4ec8-acdb-74060e241e57] initializing from _:654967f3-fadf-4ec8-acdb-74060e241e57\nDEBUG cwltool:command_line_tool.py:988 [job _:654967f3-fadf-4ec8-acdb-74060e241e57] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:654967f3-fadf-4ec8-acdb-74060e241e57] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:654967f3-fadf-4ec8-acdb-74060e241e57] command line bindings is []')], 'duration': 0.00047671700031060027, 'start': 1685951464.256713, 'stop': 1685951464.257192, '$report_type': 'TestReport', 'item_index': 630, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_tmpdir.py::test_docker_commandLineTool_job_tmpdir_prefix + location: ('tests/test_tmpdir.py', 26, 'test_docker_commandLineTool_job_tmpdir_prefix') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_tmpdir.py::test_docker_tmpdir_prefix + location: ('tests/test_tmpdir.py', 166, 'test_docker_tmpdir_prefix') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_docker_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 166, 'test_docker_tmpdir_prefix'), 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'item_index': 626, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs + location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_target.py::test_target_packed + location: ('tests/test_target.py', 29, 'test_target_packed') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_target.py::test_target_packed', 'location': ('tests/test_target.py', 29, 'test_target_packed'), 'keywords': {'test_target_packed': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00031677999959356384, 'start': 1685951464.524877, 'stop': 1685951464.5251951, '$report_type': 'TestReport', 'item_index': 629, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_nested_workflow', 'location': ('tests/test_provenance.py', 98, 'test_nested_workflow'), 'keywords': {'test_nested_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "classout": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class",\n "basename": "Hello.class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _18] start\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step create-tar\n\x1b[1;30mINFO\x1b[0m [step create-tar] start\n\x1b[1;30mINFO\x1b[0m [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nMon Jun 5 09:51:00 CEST 2023\nMon Jun 5 09:51:00 CEST 2023\n\x1b[1;30mINFO\x1b[0m [job create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [step create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step compile\n\x1b[1;30mINFO\x1b[0m [step compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step untar\n\x1b[1;30mINFO\x1b[0m [step untar] start\n\x1b[1;30mINFO\x1b[0m [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\n\x1b[1;30mINFO\x1b[0m [job untar] completed success\n\x1b[1;30mINFO\x1b[0m [step untar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step argument\n\x1b[1;30mINFO\x1b[0m [step argument] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/openjdk:9.0.1-11-slim']\n9.0.1-11-slim: Pulling from library/openjdk\nDigest: sha256:dc239c9a17aa509d4e79dc4980e40a5f0c8af78a9bcefab2b5eedf819f702298\nStatus: Image is up to date for openjdk:9.0.1-11-slim\ndocker.io/library/openjdk:9.0.1-11-slim\n\x1b[1;30mINFO\x1b[0m [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\n\x1b[1;30mINFO\x1b[0m [job argument] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job argument] completed success\n\x1b[1;30mINFO\x1b[0m [step argument] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] completed success\n\x1b[1;30mINFO\x1b[0m [step compile] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 74ece951469a5306ac6512cff2a9f3b25b91c858 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: a0f6fb34d0ba97018b294486569ded02bb6e6e659d3e06c5de4f214582691f36 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: f0dca2f20d6e9cd7b5ca6e9ea53e3c5548164e2b77ca0b2a1f3e785ce12f314ca29d1943f80ee974373ab7ead0031aee08c07bb511c34c82cc951e3bef28c9b0 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _18] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile not ready\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step create-tar\nDEBUG cwltool:workflow_job.py:727 [step create-tar] job input {}\nDEBUG cwltool:workflow_job.py:732 [step create-tar] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step create-tar] start\nDEBUG cwltool:command_line_tool.py:982 [job create-tar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/fbd87079-fe0c-4de9-b99f-0c79323cf2c1 as part of step create-tar\nDEBUG cwltool:command_line_tool.py:988 [job create-tar] {}\nDEBUG cwltool:command_line_tool.py:1000 [job create-tar] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job create-tar] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "date\\ntar cf hello.tar Hello.java\\ndate\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job create-tar] initial work dir {\n "_:5de9498b-d23e-4bbf-b5e6-3d9459eedb80": [\n "public class Hello {\\n public static void main(String[] argv) {\\n System.out.println(\\"Hello from Java\\");\\n }\\n}\\n",\n "/private/tmp/docker_tmpkyipo8y7/Hello.java",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 4864f67aab6874db8b656c7b15bd7cfc595e9571 data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nINFO cwltool:job.py:419 [job create-tar] completed success\nDEBUG cwltool:job.py:422 [job create-tar] outputs {\n "tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step create-tar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:572 [step create-tar] completed success\nDEBUG cwltool:job.py:446 [job create-tar] Removing input staging directory /private/tmp/docker_tmpzx57hfi5\nDEBUG cwltool:job.py:454 [job create-tar] Removing temporary directory /private/tmp/docker_tmp4rtd4n2g\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step compile\nDEBUG cwltool:workflow_job.py:727 [step compile] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step compile] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step compile] start\nDEBUG cwltool:workflow_job.py:498 [workflow compile] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow compile] start\nDEBUG cwltool:workflow_job.py:777 [workflow compile] inputs {\n "ex": "Hello.java",\n "inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:610 [workflow compile] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument not ready\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step untar\nDEBUG cwltool:workflow_job.py:727 [step untar] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step untar] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step untar] start\nDEBUG cwltool:command_line_tool.py:982 [job untar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/tar-param.cwl as part of step untar\nDEBUG cwltool:command_line_tool.py:988 [job untar] {\n "extractfile": "Hello.java",\n "tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job untar] path mappings is {\n "file:///private/tmp/docker_tmpkyipo8y7/hello.tar": [\n "/private/tmp/docker_tmpkyipo8y7/hello.tar",\n "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job untar] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "tar"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "xf"\n },\n {\n "position": [\n 1,\n "tarfile"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9",\n "path": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "dirname": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134"\n }\n },\n {\n "position": [\n 2,\n "extractfile"\n ],\n "datum": "Hello.java"\n }\n]\nDEBUG cwltool:job.py:215 [job untar] initial work dir {}\nINFO cwltool:job.py:266 [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 93035905e94e150874f5a881d39f3c5c6378dd38 data/93/93035905e94e150874f5a881d39f3c5c6378dd38\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nINFO cwltool:job.py:419 [job untar] completed success\nDEBUG cwltool:job.py:422 [job untar] outputs {\n "example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step untar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step untar] completed success\nDEBUG cwltool:job.py:446 [job untar] Removing input staging directory /private/tmp/docker_tmp8uve11w8\nDEBUG cwltool:job.py:454 [job untar] Removing temporary directory /private/tmp/docker_tmpnpvtosz9\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step argument\nDEBUG cwltool:workflow_job.py:727 [step argument] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step argument] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:75 [step argument] start\nDEBUG cwltool:command_line_tool.py:982 [job argument] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/arguments.cwl as part of step argument\nDEBUG cwltool:command_line_tool.py:988 [job argument] {\n "src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job argument] path mappings is {\n "file:///private/tmp/docker_tmpc_ieg46p/Hello.java": [\n "/private/tmp/docker_tmpc_ieg46p/Hello.java",\n "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job argument] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "javac"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-d"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(runtime.outdir)"\n },\n {\n "position": [\n 1,\n "src"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5",\n "path": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "dirname": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/openjdk:9.0.1-11-slim\']\nDEBUG cwltool:job.py:215 [job argument] initial work dir {}\nINFO cwltool:job.py:266 [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\nINFO cwltool:job.py:905 [job argument] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 39e3219327347c05aa3e82236f83aa6d77fe6bfd data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nINFO cwltool:job.py:419 [job argument] completed success\nDEBUG cwltool:job.py:422 [job argument] outputs {\n "classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step argument] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step argument] completed success\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 83049fca7761d12fb0a5da48da3c037c5304a0fc metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 60258aab9b1b640774e4705795ed3f7ae538c98238f3fae97911d4b93bbfaa2d metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 33139ea057934520ce5f2525af14fafb879322770000acdb150ee5aa445568f3588850a5f5951dce7a03937af0e4ae1ecddafaff17b8299b4e9b2d2372aa07e7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0304d4e8c149fbe870496f20f4c073b6946f7fe7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 13120ba16180324a0c690989fede01b2424adce87145cd0da6492b177f8f814c metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 86e81f57bbb1e5335d9dd2921076dfeba39e953bc4214261e7d818a3a7f38ebb9c4367320cf6fa2714c96e00132009d102c6b6604f36fefc1639cdb722d70715 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: cff4ad2216ea628f4975c69699c8e3fc0c3e4632 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 5d742295d8aba73c67424e366c394e0a34f773985c1645c9b6910e35e353afc9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c6b20c2741a3fa0edeb70054d7f72885b90dd62331b41d5f9fb9f2032495d78b83428995111a6ba52d098f57d976c760321811e6ea182d2e2f562976ba5ad1c9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 1fdf97a3b214d0a050db07a554ecfe44b056e655 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 325d75d9f711a5a12feee43188da250d5fdc200b6ca2e33214209fed193a87c8 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8cac58c921bd6a7115ef1dace866bdb2b84dd948cbed5014ab70eae79abe7b30e8ddeafc033659ddb581ac53550230aa818e3623fc55cebae094df17b7b9cd64 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9f2ad16a37a1df641dfe180c8704e88211c46676 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 939e5a54c9079007e36c852408057047622c11cb1d06b2b64b82636d8a1d6762 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 65707a62469cf55e9dcb8fdfe87bf1af958df3846a5de0a6c4732557af5ad6ddfd07fae87e80e7c4c3cef36d0b3b25b03293a5805ddeecf1d86980a7bff1e885 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9be8dfc973c5248324d388bda772ced2eafc5d09 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 4ad66e5bea19ad398ad45267244c6fb7e950340d509df851edbad2fbb844a504 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 63e5b105c46bef759931359c5994f6cff8029bb8a59911a3458df8d1e4e1b98fb3b6f8689c2096670880e2833bd3ae7e369b8e77ef0c7ae613edb86ff6dd9887 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nINFO cwltool:workflow_job.py:539 [workflow compile] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow compile] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step compile] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step compile] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:job.py:446 [job argument] Removing input staging directory /private/tmp/docker_tmpebe5z0v8\nDEBUG cwltool:job.py:454 [job argument] Removing temporary directory /private/tmp/docker_tmpdff4tkfu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpepzg_f_c/Hello.class to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzrpr1a4o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr_sgrnnb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpepzg_f_c\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkyipo8y7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpc_ieg46p\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 19fbff09cc97d57d7241305ed0cb03212f211ae9 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 410b6c9c1c10cc229c8781ddc5074f25f371cdf9b4e6e053758e98931db2f7eb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 6c75e7c3ef6bf96b917b3961bf1350658fec598fb67d194716c7fa281d09ae834cf81cea64f8636e34b2a8391b8d4391e267b526d90b3460ed50ffa35b615b9f metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 42906be32350038218f034e2418bfa414323fecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 54d1a6a2ea333664645b1ef510288b473b2798d0eba102c7d9f83979acdb30ea metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 59de6004ed6286c5bf4461690f1eea3eecec94be8cf7f186aa9100dd447ed2d3f8e78d8bb9a09b712d6bf0c16f036559fb76f2e57f9c9bf47f5b868d5a5b1698 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 54936279704d89dd038e6bb6207276b94ccf52c7 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48a6d44504c674c65ae71bf0186c051343568e8b1796272af0adf58b39dfc015 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 77323c4d9ca07d91bcb9db9f7090422963c30ec31c9cc7312a2619f60dfb0f8632630019a19f57fd3f2bbe2a354d0328dfb60c482f81141a31ea1b3c118e2466 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 76273be200ec2c229e213509b9bb670478dce7f4 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48244946e314f094d1b6c4b6e30a3358b5cbca006e442806c064eb0ffb961c1a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 64a2901aa5304fa5d65408f3a61b12c9131f251d89f4e688f9c3c3cdcba700f7fc67069606af5b24e6196f60e2553a53f51fda4ff970d89a7d91881ff5ffc4b5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: d80b34fd80aa3f9137314feb7021908e2b52cb91 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cc95cb90e86609a55c17cd318a3e5bd9892687cc6df9ba66fc8479dfd0d95aef metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 697c8c7b70137288a5672502d3786e77f04ce6f28f5a549ac71edb9f8bac64d7cb6ee4ef13ce84d9184f865db3ccaa66cf20bc62f31824e4b558a9bb959d6ef4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: f8b1b468869ac1a80043e092868c2277f1d15c64 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1805212079569e9a572fab9cdb3b73665e98e5ca3ec88d9b637ee30ffd026e11 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 036d8f071535a67857917407770951d720c444f3b9057b0bd8194be89066977bcc223f1ad268b552ea07d143c886679c4cbb66d79a0dea214672d54ec41358ff metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'classout\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello.class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 419\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a77f1bf715803e410ab8646eec4bee4f620aca8f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 023017d52b11f799321c82c33eb3f4b053ed57872618d37d30b69ec0c64902f8 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8e911b78c78b0a5146fc24f8adbdf1f253a2d78f6239c81533b0166ebd4f7ed7dd64e7fb3f86a7f62eb6d4288ade648629ef6c28ad1ab4accadc2800a8038123 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 724b068a51d129c5492f28865b3bed0eb22a8dec snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 0727286ce68bebcae06f0cb1da28a58382c9db14f0e4eae7e29f5644483d16cb snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c116c653cd68a7fd934d7df77d24a4977efa1c6505d6c32b138aec44130d40228f7d69bf3b11fb9473e421755e7d592f15b1aa93c988b1ec3249dc84139b7960 snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 7b997f5397fd668969634a4e8c113cec0fbbc5e8 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cdd580b6c0f37c60cc39ef4968184235ade6ab7369329b363c5db7f101f6d3a4 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 3c72796915141289f4e94ec0b83fa5fbd0203d8afb69adf0dcd866a616ddc9a432d071e75e54f3eafcd3d850411b6cfb54643cf123fb246206f49885a0b5fdbf snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b9b609b8713bd5ebed4e83e8074f84648a5f6708 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 6ddc89e25e65a9a6e80de48be06442cef0128b9f1c82ec8d50019223c5bfd866 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 58e44c861533f86faee277fc618bd869781ec5c1203bad37d150dd5efaed44d51198c9fed40ddd62b9ef348e2a9b9f5004d86c9983ee22ac61070b0c588a8229 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a11e6ae3b6824babd50ca5a96395030d203565f6 snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ba73050af0d17a6a24d82aeb88b54150e38189056007f1dd094a59562f30475d snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 57fe970c776bf2b8f283783b6565d886acd7f5974ec7a7a9de547201585a93130c40b494e29bb2a489123dc5d0c30f791c585f1f29dc11ff8d381b16c7d9e348 snapshot/tar-param.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0dd82b60f74970af2204ec209f5d9ba9bcf90ab1 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1991adaba7d0cdd01efb884f896e70162a678d6c019c8af40a628e3e81c958dd metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c8b1f27a515fda5fffc55d93abf31ae91d00fe9077046e16109522c83fd5740e4df390bb7dce1e8d7c5ee00e3d1532e298ee248addec8623f2d88f1f0b5d94d4 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b201b1900b531a5cac833222efcf2ea148ee8e4f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: be90e3007275188cbc913e1d8e0b2901a70917ecb0c4d82a9967a894ad18fc33 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca20cd4c002dea5a664c54c7a7d874ed07461ed50baf0016e4e9c45fdaa16132772748146c0f39bf409004e80e3c2ee9db16490543e86a8e41e45cea5758d3af metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 8e62f08782410be5f7a325ad891118c1c8b048c9 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: af35cf1992cf37219396ab2b24f2c0bc89e1e9d3fa27c63d3f8c8a2a64c2b62a bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c3bdb2ec78cc257d15b637073d81804b259e9bd197b9b0aa71d9a3b66b7eee0df29dbd0f6146ebdb9fee6e3adc073a09a3cd260708cc7890a982c547bb28d165 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance')], 'duration': 5.002003371999308, 'start': 1685951459.705703, 'stop': 1685951464.707586, '$report_type': 'TestReport', 'item_index': 527, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_nested_workflow', 'location': ('tests/test_provenance.py', 98, 'test_nested_workflow'), 'keywords': {'test_nested_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "classout": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class",\n "basename": "Hello.class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _18] start\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step create-tar\n\x1b[1;30mINFO\x1b[0m [step create-tar] start\n\x1b[1;30mINFO\x1b[0m [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nMon Jun 5 09:51:00 CEST 2023\nMon Jun 5 09:51:00 CEST 2023\n\x1b[1;30mINFO\x1b[0m [job create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [step create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step compile\n\x1b[1;30mINFO\x1b[0m [step compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step untar\n\x1b[1;30mINFO\x1b[0m [step untar] start\n\x1b[1;30mINFO\x1b[0m [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\n\x1b[1;30mINFO\x1b[0m [job untar] completed success\n\x1b[1;30mINFO\x1b[0m [step untar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step argument\n\x1b[1;30mINFO\x1b[0m [step argument] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/openjdk:9.0.1-11-slim']\n9.0.1-11-slim: Pulling from library/openjdk\nDigest: sha256:dc239c9a17aa509d4e79dc4980e40a5f0c8af78a9bcefab2b5eedf819f702298\nStatus: Image is up to date for openjdk:9.0.1-11-slim\ndocker.io/library/openjdk:9.0.1-11-slim\n\x1b[1;30mINFO\x1b[0m [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\n\x1b[1;30mINFO\x1b[0m [job argument] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job argument] completed success\n\x1b[1;30mINFO\x1b[0m [step argument] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] completed success\n\x1b[1;30mINFO\x1b[0m [step compile] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 74ece951469a5306ac6512cff2a9f3b25b91c858 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: a0f6fb34d0ba97018b294486569ded02bb6e6e659d3e06c5de4f214582691f36 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: f0dca2f20d6e9cd7b5ca6e9ea53e3c5548164e2b77ca0b2a1f3e785ce12f314ca29d1943f80ee974373ab7ead0031aee08c07bb511c34c82cc951e3bef28c9b0 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _18] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile not ready\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step create-tar\nDEBUG cwltool:workflow_job.py:727 [step create-tar] job input {}\nDEBUG cwltool:workflow_job.py:732 [step create-tar] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step create-tar] start\nDEBUG cwltool:command_line_tool.py:982 [job create-tar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/fbd87079-fe0c-4de9-b99f-0c79323cf2c1 as part of step create-tar\nDEBUG cwltool:command_line_tool.py:988 [job create-tar] {}\nDEBUG cwltool:command_line_tool.py:1000 [job create-tar] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job create-tar] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "date\\ntar cf hello.tar Hello.java\\ndate\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job create-tar] initial work dir {\n "_:5de9498b-d23e-4bbf-b5e6-3d9459eedb80": [\n "public class Hello {\\n public static void main(String[] argv) {\\n System.out.println(\\"Hello from Java\\");\\n }\\n}\\n",\n "/private/tmp/docker_tmpkyipo8y7/Hello.java",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 4864f67aab6874db8b656c7b15bd7cfc595e9571 data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nINFO cwltool:job.py:419 [job create-tar] completed success\nDEBUG cwltool:job.py:422 [job create-tar] outputs {\n "tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step create-tar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:572 [step create-tar] completed success\nDEBUG cwltool:job.py:446 [job create-tar] Removing input staging directory /private/tmp/docker_tmpzx57hfi5\nDEBUG cwltool:job.py:454 [job create-tar] Removing temporary directory /private/tmp/docker_tmp4rtd4n2g\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step compile\nDEBUG cwltool:workflow_job.py:727 [step compile] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step compile] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step compile] start\nDEBUG cwltool:workflow_job.py:498 [workflow compile] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow compile] start\nDEBUG cwltool:workflow_job.py:777 [workflow compile] inputs {\n "ex": "Hello.java",\n "inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:610 [workflow compile] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument not ready\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step untar\nDEBUG cwltool:workflow_job.py:727 [step untar] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step untar] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step untar] start\nDEBUG cwltool:command_line_tool.py:982 [job untar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/tar-param.cwl as part of step untar\nDEBUG cwltool:command_line_tool.py:988 [job untar] {\n "extractfile": "Hello.java",\n "tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job untar] path mappings is {\n "file:///private/tmp/docker_tmpkyipo8y7/hello.tar": [\n "/private/tmp/docker_tmpkyipo8y7/hello.tar",\n "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job untar] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "tar"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "xf"\n },\n {\n "position": [\n 1,\n "tarfile"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9",\n "path": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "dirname": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134"\n }\n },\n {\n "position": [\n 2,\n "extractfile"\n ],\n "datum": "Hello.java"\n }\n]\nDEBUG cwltool:job.py:215 [job untar] initial work dir {}\nINFO cwltool:job.py:266 [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 93035905e94e150874f5a881d39f3c5c6378dd38 data/93/93035905e94e150874f5a881d39f3c5c6378dd38\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nINFO cwltool:job.py:419 [job untar] completed success\nDEBUG cwltool:job.py:422 [job untar] outputs {\n "example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step untar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step untar] completed success\nDEBUG cwltool:job.py:446 [job untar] Removing input staging directory /private/tmp/docker_tmp8uve11w8\nDEBUG cwltool:job.py:454 [job untar] Removing temporary directory /private/tmp/docker_tmpnpvtosz9\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step argument\nDEBUG cwltool:workflow_job.py:727 [step argument] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step argument] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:75 [step argument] start\nDEBUG cwltool:command_line_tool.py:982 [job argument] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/arguments.cwl as part of step argument\nDEBUG cwltool:command_line_tool.py:988 [job argument] {\n "src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job argument] path mappings is {\n "file:///private/tmp/docker_tmpc_ieg46p/Hello.java": [\n "/private/tmp/docker_tmpc_ieg46p/Hello.java",\n "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job argument] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "javac"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-d"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(runtime.outdir)"\n },\n {\n "position": [\n 1,\n "src"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5",\n "path": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "dirname": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/openjdk:9.0.1-11-slim\']\nDEBUG cwltool:job.py:215 [job argument] initial work dir {}\nINFO cwltool:job.py:266 [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\nINFO cwltool:job.py:905 [job argument] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 39e3219327347c05aa3e82236f83aa6d77fe6bfd data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nINFO cwltool:job.py:419 [job argument] completed success\nDEBUG cwltool:job.py:422 [job argument] outputs {\n "classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step argument] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step argument] completed success\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 83049fca7761d12fb0a5da48da3c037c5304a0fc metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 60258aab9b1b640774e4705795ed3f7ae538c98238f3fae97911d4b93bbfaa2d metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 33139ea057934520ce5f2525af14fafb879322770000acdb150ee5aa445568f3588850a5f5951dce7a03937af0e4ae1ecddafaff17b8299b4e9b2d2372aa07e7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0304d4e8c149fbe870496f20f4c073b6946f7fe7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 13120ba16180324a0c690989fede01b2424adce87145cd0da6492b177f8f814c metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 86e81f57bbb1e5335d9dd2921076dfeba39e953bc4214261e7d818a3a7f38ebb9c4367320cf6fa2714c96e00132009d102c6b6604f36fefc1639cdb722d70715 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: cff4ad2216ea628f4975c69699c8e3fc0c3e4632 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 5d742295d8aba73c67424e366c394e0a34f773985c1645c9b6910e35e353afc9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c6b20c2741a3fa0edeb70054d7f72885b90dd62331b41d5f9fb9f2032495d78b83428995111a6ba52d098f57d976c760321811e6ea182d2e2f562976ba5ad1c9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 1fdf97a3b214d0a050db07a554ecfe44b056e655 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 325d75d9f711a5a12feee43188da250d5fdc200b6ca2e33214209fed193a87c8 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8cac58c921bd6a7115ef1dace866bdb2b84dd948cbed5014ab70eae79abe7b30e8ddeafc033659ddb581ac53550230aa818e3623fc55cebae094df17b7b9cd64 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9f2ad16a37a1df641dfe180c8704e88211c46676 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 939e5a54c9079007e36c852408057047622c11cb1d06b2b64b82636d8a1d6762 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 65707a62469cf55e9dcb8fdfe87bf1af958df3846a5de0a6c4732557af5ad6ddfd07fae87e80e7c4c3cef36d0b3b25b03293a5805ddeecf1d86980a7bff1e885 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9be8dfc973c5248324d388bda772ced2eafc5d09 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 4ad66e5bea19ad398ad45267244c6fb7e950340d509df851edbad2fbb844a504 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 63e5b105c46bef759931359c5994f6cff8029bb8a59911a3458df8d1e4e1b98fb3b6f8689c2096670880e2833bd3ae7e369b8e77ef0c7ae613edb86ff6dd9887 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nINFO cwltool:workflow_job.py:539 [workflow compile] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow compile] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step compile] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step compile] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:job.py:446 [job argument] Removing input staging directory /private/tmp/docker_tmpebe5z0v8\nDEBUG cwltool:job.py:454 [job argument] Removing temporary directory /private/tmp/docker_tmpdff4tkfu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpepzg_f_c/Hello.class to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzrpr1a4o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr_sgrnnb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpepzg_f_c\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkyipo8y7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpc_ieg46p\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 19fbff09cc97d57d7241305ed0cb03212f211ae9 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 410b6c9c1c10cc229c8781ddc5074f25f371cdf9b4e6e053758e98931db2f7eb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 6c75e7c3ef6bf96b917b3961bf1350658fec598fb67d194716c7fa281d09ae834cf81cea64f8636e34b2a8391b8d4391e267b526d90b3460ed50ffa35b615b9f metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 42906be32350038218f034e2418bfa414323fecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 54d1a6a2ea333664645b1ef510288b473b2798d0eba102c7d9f83979acdb30ea metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 59de6004ed6286c5bf4461690f1eea3eecec94be8cf7f186aa9100dd447ed2d3f8e78d8bb9a09b712d6bf0c16f036559fb76f2e57f9c9bf47f5b868d5a5b1698 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 54936279704d89dd038e6bb6207276b94ccf52c7 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48a6d44504c674c65ae71bf0186c051343568e8b1796272af0adf58b39dfc015 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 77323c4d9ca07d91bcb9db9f7090422963c30ec31c9cc7312a2619f60dfb0f8632630019a19f57fd3f2bbe2a354d0328dfb60c482f81141a31ea1b3c118e2466 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 76273be200ec2c229e213509b9bb670478dce7f4 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48244946e314f094d1b6c4b6e30a3358b5cbca006e442806c064eb0ffb961c1a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 64a2901aa5304fa5d65408f3a61b12c9131f251d89f4e688f9c3c3cdcba700f7fc67069606af5b24e6196f60e2553a53f51fda4ff970d89a7d91881ff5ffc4b5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: d80b34fd80aa3f9137314feb7021908e2b52cb91 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cc95cb90e86609a55c17cd318a3e5bd9892687cc6df9ba66fc8479dfd0d95aef metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 697c8c7b70137288a5672502d3786e77f04ce6f28f5a549ac71edb9f8bac64d7cb6ee4ef13ce84d9184f865db3ccaa66cf20bc62f31824e4b558a9bb959d6ef4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: f8b1b468869ac1a80043e092868c2277f1d15c64 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1805212079569e9a572fab9cdb3b73665e98e5ca3ec88d9b637ee30ffd026e11 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 036d8f071535a67857917407770951d720c444f3b9057b0bd8194be89066977bcc223f1ad268b552ea07d143c886679c4cbb66d79a0dea214672d54ec41358ff metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'classout\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello.class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 419\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a77f1bf715803e410ab8646eec4bee4f620aca8f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 023017d52b11f799321c82c33eb3f4b053ed57872618d37d30b69ec0c64902f8 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8e911b78c78b0a5146fc24f8adbdf1f253a2d78f6239c81533b0166ebd4f7ed7dd64e7fb3f86a7f62eb6d4288ade648629ef6c28ad1ab4accadc2800a8038123 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 724b068a51d129c5492f28865b3bed0eb22a8dec snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 0727286ce68bebcae06f0cb1da28a58382c9db14f0e4eae7e29f5644483d16cb snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c116c653cd68a7fd934d7df77d24a4977efa1c6505d6c32b138aec44130d40228f7d69bf3b11fb9473e421755e7d592f15b1aa93c988b1ec3249dc84139b7960 snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 7b997f5397fd668969634a4e8c113cec0fbbc5e8 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cdd580b6c0f37c60cc39ef4968184235ade6ab7369329b363c5db7f101f6d3a4 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 3c72796915141289f4e94ec0b83fa5fbd0203d8afb69adf0dcd866a616ddc9a432d071e75e54f3eafcd3d850411b6cfb54643cf123fb246206f49885a0b5fdbf snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b9b609b8713bd5ebed4e83e8074f84648a5f6708 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 6ddc89e25e65a9a6e80de48be06442cef0128b9f1c82ec8d50019223c5bfd866 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 58e44c861533f86faee277fc618bd869781ec5c1203bad37d150dd5efaed44d51198c9fed40ddd62b9ef348e2a9b9f5004d86c9983ee22ac61070b0c588a8229 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a11e6ae3b6824babd50ca5a96395030d203565f6 snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ba73050af0d17a6a24d82aeb88b54150e38189056007f1dd094a59562f30475d snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 57fe970c776bf2b8f283783b6565d886acd7f5974ec7a7a9de547201585a93130c40b494e29bb2a489123dc5d0c30f791c585f1f29dc11ff8d381b16c7d9e348 snapshot/tar-param.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0dd82b60f74970af2204ec209f5d9ba9bcf90ab1 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1991adaba7d0cdd01efb884f896e70162a678d6c019c8af40a628e3e81c958dd metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c8b1f27a515fda5fffc55d93abf31ae91d00fe9077046e16109522c83fd5740e4df390bb7dce1e8d7c5ee00e3d1532e298ee248addec8623f2d88f1f0b5d94d4 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b201b1900b531a5cac833222efcf2ea148ee8e4f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: be90e3007275188cbc913e1d8e0b2901a70917ecb0c4d82a9967a894ad18fc33 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca20cd4c002dea5a664c54c7a7d874ed07461ed50baf0016e4e9c45fdaa16132772748146c0f39bf409004e80e3c2ee9db16490543e86a8e41e45cea5758d3af metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 8e62f08782410be5f7a325ad891118c1c8b048c9 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: af35cf1992cf37219396ab2b24f2c0bc89e1e9d3fa27c63d3f8c8a2a64c2b62a bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c3bdb2ec78cc257d15b637073d81804b259e9bd197b9b0aa71d9a3b66b7eee0df29dbd0f6146ebdb9fee6e3adc073a09a3cd260708cc7890a982c547bb28d165 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance')], 'duration': 0.00113051800053654, 'start': 1685951464.710773, 'stop': 1685951464.711905, '$report_type': 'TestReport', 'item_index': 527, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_nested_workflow + location: ('tests/test_provenance.py', 98, 'test_nested_workflow') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + when: runtest + nodeid: tests/test_provenance.py::test_nested_workflow + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_secondary_files_implicit + location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_implicit', 'location': ('tests/test_provenance.py', 103, 'test_secondary_files_implicit'), 'keywords': {'test_secondary_files_implicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012492460000430583, 'start': 1685951464.7161531, 'stop': 1685951464.717403, '$report_type': 'TestReport', 'item_index': 528, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_remove_tmpdirs', 'location': ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs'), 'keywords': {'test_remove_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nHello\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello"\n }\n]\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/2yfuzdes\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/a2i94b9v\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6808559439996316, 'start': 1685951464.298953, 'stop': 1685951464.979794, '$report_type': 'TestReport', 'item_index': 636, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_remove_tmpdirs', 'location': ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs'), 'keywords': {'test_remove_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nHello\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello"\n }\n]\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/2yfuzdes\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/a2i94b9v\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005884539996259264, 'start': 1685951464.980832, 'stop': 1685951464.9814222, '$report_type': 'TestReport', 'item_index': 636, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_tmpdir.py::test_remove_tmpdirs + location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_tmpdir.py::test_leave_tmpdirs + location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_leave_tmpdirs', 'location': ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs'), 'keywords': {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016575850004301174, 'start': 1685951464.983828, 'stop': 1685951464.9854872, '$report_type': 'TestReport', 'item_index': 637, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_target.py::test_target', 'location': ('tests/test_target.py', 5, 'test_target'), 'keywords': {'test_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _22] start\n\x1b[1;30mINFO\x1b[0m [workflow _22] starting step step1_5\n\x1b[1;30mINFO\x1b[0m [step step1_5] start\n\x1b[1;30mINFO\x1b[0m [job step1_4] /private/tmp/docker_tmpzwwa6z6d$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpzwwa6z6d/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_4] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _22] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _22] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _22] start\nDEBUG cwltool:workflow_job.py:777 [workflow _22] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _22] starting step step1_5\nINFO cwltool:workflow_job.py:75 [step step1_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_5\nDEBUG cwltool:command_line_tool.py:988 [job step1_4] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_4] initial work dir {}\nINFO cwltool:job.py:266 [job step1_4] /private/tmp/docker_tmpzwwa6z6d$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpzwwa6z6d/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_4] completed success\nDEBUG cwltool:job.py:422 [job step1_4] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow _22] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _22] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_4] Removing input staging directory /private/tmp/docker_tmpr5xvimrj\nDEBUG cwltool:job.py:454 [job step1_4] Removing temporary directory /private/tmp/docker_tmpk8t9sgbi\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpd528_x8e\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzwwa6z6d\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.602284578999388, 'start': 1685951463.50167, 'stop': 1685951465.103916, '$report_type': 'TestReport', 'item_index': 627, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_target.py::test_target', 'location': ('tests/test_target.py', 5, 'test_target'), 'keywords': {'test_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _22] start\n\x1b[1;30mINFO\x1b[0m [workflow _22] starting step step1_5\n\x1b[1;30mINFO\x1b[0m [step step1_5] start\n\x1b[1;30mINFO\x1b[0m [job step1_4] /private/tmp/docker_tmpzwwa6z6d$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpzwwa6z6d/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_4] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _22] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _22] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _22] start\nDEBUG cwltool:workflow_job.py:777 [workflow _22] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _22] starting step step1_5\nINFO cwltool:workflow_job.py:75 [step step1_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_5\nDEBUG cwltool:command_line_tool.py:988 [job step1_4] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_4] initial work dir {}\nINFO cwltool:job.py:266 [job step1_4] /private/tmp/docker_tmpzwwa6z6d$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpzwwa6z6d/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_4] completed success\nDEBUG cwltool:job.py:422 [job step1_4] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow _22] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _22] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_4] Removing input staging directory /private/tmp/docker_tmpr5xvimrj\nDEBUG cwltool:job.py:454 [job step1_4] Removing temporary directory /private/tmp/docker_tmpk8t9sgbi\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpd528_x8e\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzwwa6z6d\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005301219998727902, 'start': 1685951465.1055648, 'stop': 1685951465.106097, '$report_type': 'TestReport', 'item_index': 627, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_target.py::test_target + location: ('tests/test_target.py', 5, 'test_target') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_tmpdir.py::test_commandLineTool_job_tmpdir_prefix + location: ('tests/test_tmpdir.py', 71, 'test_commandLineTool_job_tmpdir_prefix') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_commandLineTool_job_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 71, 'test_commandLineTool_job_tmpdir_prefix'), 'keywords': {'test_commandLineTool_job_tmpdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016978080002445495, 'start': 1685951465.108722, 'stop': 1685951465.1104221, '$report_type': 'TestReport', 'item_index': 631, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_commandLineTool_job_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 71, 'test_commandLineTool_job_tmpdir_prefix'), 'keywords': {'test_commandLineTool_job_tmpdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] initializing from _:970a4ffb-1255-4205-8526-cc9a0ae3a187\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] initializing from _:970a4ffb-1255-4205-8526-cc9a0ae3a187\nDEBUG cwltool:command_line_tool.py:988 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] command line bindings is []')], 'duration': 0.0059925939995082445, 'start': 1685951465.111041, 'stop': 1685951465.117035, '$report_type': 'TestReport', 'item_index': 631, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_commandLineTool_job_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 71, 'test_commandLineTool_job_tmpdir_prefix'), 'keywords': {'test_commandLineTool_job_tmpdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] initializing from _:970a4ffb-1255-4205-8526-cc9a0ae3a187\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:05]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] initializing from _:970a4ffb-1255-4205-8526-cc9a0ae3a187\nDEBUG cwltool:command_line_tool.py:988 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:970a4ffb-1255-4205-8526-cc9a0ae3a187] command line bindings is []')], 'duration': 0.00030151900045893854, 'start': 1685951465.1175349, 'stop': 1685951465.1178381, '$report_type': 'TestReport', 'item_index': 631, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_tmpdir.py::test_commandLineTool_job_tmpdir_prefix + location: ('tests/test_tmpdir.py', 71, 'test_commandLineTool_job_tmpdir_prefix') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00162337599977036, 'start': 1685951465.1201751, 'stop': 1685951465.1218, '$report_type': 'TestReport', 'item_index': 641, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '"test"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script",\n "foo": {\n "one": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n },\n "two": "test"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpsxld0jq6\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script",\n "foo": {\n "one": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n },\n "two": "test"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsxld0jq6\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6780413209999097, 'start': 1685951465.1225579, 'stop': 1685951465.8005838, '$report_type': 'TestReport', 'item_index': 641, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '"test"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script",\n "foo": {\n "one": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n },\n "two": "test"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpsxld0jq6\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script",\n "foo": {\n "one": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n },\n "two": "test"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsxld0jq6\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005465860003823764, 'start': 1685951465.8011048, 'stop': 1685951465.801653, '$report_type': 'TestReport', 'item_index': 641, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_implicit', 'location': ('tests/test_provenance.py', 103, 'test_secondary_files_implicit'), 'keywords': {'test_secondary_files_implicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'--file1\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7fbe1688c021dd47067816cb1915f194a21b192a workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: fdd353f2fc1a5ce060db48433d4c5d39841c3a16a7b3859ecf40c5d0559585cb workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5af67683ddcf0dc25317f9299432e1b480cba92fefc530bb82144c0b46d090163964253480d1d2b57d8d93bc800be27c6a17552dff8d5d285dfea3792633143a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx",\n "size": 3\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpwlagwb74\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpneari7wr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmprjpz3kex\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm23vbaqp\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b4bef5453619901d1f8f99b5ae6de84b0d9e639b metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 5db39cc34f5ff26b64a03b03b9101fecc2312db65289fe2d1be735727992d8bd metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 8d283d305c0e6d11608b05d9a5e1ba5a75fb4aba75402c34b62e6d7daa1524e3e4995c7b5b7dd09e2e1b461a78c125bc27d82023ed600a5efe3ca285ad10ea97 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 8727ee5875ce1f873aaea8acd610451c6f552485 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 7ea7c1f314778c5b956cac5c77bce95ea6b88611ebbc7066030f869d1db4451d metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: bfc8b1282a1fb06945d4fe7918b05d4f0406bbf7cb97de9e7fc3a34a9d24662816b96a4494d9a1063a86717119f908eb3bf90fe45fe4ef1c346c31b9266615c3 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 137c02dbe6b251a0db3df717988e236021b8999b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 563c5a34f521209ac347f8053149f64041ee7b452c394b4d8c04be39be52d09c metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 2eb1f8f6df902d2db5dab2f042daad6a2b591ba84f6017b4920c49d9a72328f2c0e3b8624a9d3b4740645ab3df6fcbfea29f90b796df9be09a37cf9d455769dc metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: f958ba8327cc8b9af11b209e763c08fd828c4aae metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9eee73bac677248e20e3fdc1b3945afaa24f84f31779a432ecc800f5959ac994 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 98aff7bc546d9f42dfcb7cfc86031061cd09819e93cafb46dea0818f5f55023540eed22292a07e8cbee2e3b5a0a3da1b5096d16a38d308112c5b359c4a7e66ef metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 28ac6c4bb8ee879415c09c5c428f9e146863163b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd2b49ac8dce047e8c28351499fefd31d5acd14bd37d5bbb2a984b091accd35d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5a11c7149e3fe38c8365859626f63e90a4a2edbd1603d17ab341ef329bbe5a0b5408df2f612212175eec6fef219878b2cd631e8924ff2f66fab9df76f87a5d2b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 52e03863abba9f946950a2419bc5a3c9d593fd04 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 8e79daf03e3958103d27e310d0879c8812989df38d007346f55fb9433c4108c8 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 00f022778fd2a8b71a936a2bb5b382645d9663735588b29c3a4228989d43026867c3654b71a7087b9bdd09ebcdf95d5e97d22cabef6d0404bff05a436c15996b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 4b5fce360bf0db096420ddf360cb05fb63abef9a metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 12c59130a589553031e8a732559d20225da263aa19d2b43b4f23f2ff47a13396 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: a0f2b7ecf70b39b1e7b84ddab845455bf81f04019ecf1810b9540809be18cfb5a5fcdeb90986c4b11d0d86c85d38ced387beb5248a97e75460019687346cca41 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7da08c3bcf057f5790aae85a316cc4c7e84e8dae metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9822a8bb8f23ff4a5f546df0e1901dac8ce404c90cc9e864c932e858f342296c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 20961f19fd0db8bf533ce8aa98d561c15d672364183fc007e488c01e40271698363b6d1e35edfd4d109b9863391b666e44cb49cbec572343804ee8aec795de28 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3a83e9297c5eca6e6de723837360f84464d4ee94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 57f04fd3cbd44703b65a45ec0acd6b1e56243dd599476dff375f2c868198939d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 7eca04aa9b2734f1b61e65c7f009cd6ddd45735a0c303dd0653b766f411e9fdea1255c5db384dd0b3f787f5b1920fbacdea475948ad439ac70e2589a09f42b46 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance')], 'duration': 1.082738922000317, 'start': 1685951464.7178009, 'stop': 1685951465.800514, '$report_type': 'TestReport', 'item_index': 528, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_implicit', 'location': ('tests/test_provenance.py', 103, 'test_secondary_files_implicit'), 'keywords': {'test_secondary_files_implicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'--file1\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7fbe1688c021dd47067816cb1915f194a21b192a workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: fdd353f2fc1a5ce060db48433d4c5d39841c3a16a7b3859ecf40c5d0559585cb workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5af67683ddcf0dc25317f9299432e1b480cba92fefc530bb82144c0b46d090163964253480d1d2b57d8d93bc800be27c6a17552dff8d5d285dfea3792633143a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx",\n "size": 3\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpwlagwb74\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpneari7wr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmprjpz3kex\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm23vbaqp\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b4bef5453619901d1f8f99b5ae6de84b0d9e639b metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 5db39cc34f5ff26b64a03b03b9101fecc2312db65289fe2d1be735727992d8bd metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 8d283d305c0e6d11608b05d9a5e1ba5a75fb4aba75402c34b62e6d7daa1524e3e4995c7b5b7dd09e2e1b461a78c125bc27d82023ed600a5efe3ca285ad10ea97 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 8727ee5875ce1f873aaea8acd610451c6f552485 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 7ea7c1f314778c5b956cac5c77bce95ea6b88611ebbc7066030f869d1db4451d metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: bfc8b1282a1fb06945d4fe7918b05d4f0406bbf7cb97de9e7fc3a34a9d24662816b96a4494d9a1063a86717119f908eb3bf90fe45fe4ef1c346c31b9266615c3 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 137c02dbe6b251a0db3df717988e236021b8999b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 563c5a34f521209ac347f8053149f64041ee7b452c394b4d8c04be39be52d09c metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 2eb1f8f6df902d2db5dab2f042daad6a2b591ba84f6017b4920c49d9a72328f2c0e3b8624a9d3b4740645ab3df6fcbfea29f90b796df9be09a37cf9d455769dc metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: f958ba8327cc8b9af11b209e763c08fd828c4aae metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9eee73bac677248e20e3fdc1b3945afaa24f84f31779a432ecc800f5959ac994 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 98aff7bc546d9f42dfcb7cfc86031061cd09819e93cafb46dea0818f5f55023540eed22292a07e8cbee2e3b5a0a3da1b5096d16a38d308112c5b359c4a7e66ef metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 28ac6c4bb8ee879415c09c5c428f9e146863163b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd2b49ac8dce047e8c28351499fefd31d5acd14bd37d5bbb2a984b091accd35d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5a11c7149e3fe38c8365859626f63e90a4a2edbd1603d17ab341ef329bbe5a0b5408df2f612212175eec6fef219878b2cd631e8924ff2f66fab9df76f87a5d2b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 52e03863abba9f946950a2419bc5a3c9d593fd04 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 8e79daf03e3958103d27e310d0879c8812989df38d007346f55fb9433c4108c8 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 00f022778fd2a8b71a936a2bb5b382645d9663735588b29c3a4228989d43026867c3654b71a7087b9bdd09ebcdf95d5e97d22cabef6d0404bff05a436c15996b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 4b5fce360bf0db096420ddf360cb05fb63abef9a metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 12c59130a589553031e8a732559d20225da263aa19d2b43b4f23f2ff47a13396 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: a0f2b7ecf70b39b1e7b84ddab845455bf81f04019ecf1810b9540809be18cfb5a5fcdeb90986c4b11d0d86c85d38ced387beb5248a97e75460019687346cca41 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7da08c3bcf057f5790aae85a316cc4c7e84e8dae metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9822a8bb8f23ff4a5f546df0e1901dac8ce404c90cc9e864c932e858f342296c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 20961f19fd0db8bf533ce8aa98d561c15d672364183fc007e488c01e40271698363b6d1e35edfd4d109b9863391b666e44cb49cbec572343804ee8aec795de28 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3a83e9297c5eca6e6de723837360f84464d4ee94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 57f04fd3cbd44703b65a45ec0acd6b1e56243dd599476dff375f2c868198939d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 7eca04aa9b2734f1b61e65c7f009cd6ddd45735a0c303dd0653b766f411e9fdea1255c5db384dd0b3f787f5b1920fbacdea475948ad439ac70e2589a09f42b46 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance')], 'duration': 0.0008646879996376811, 'start': 1685951465.802495, 'stop': 1685951465.803361, '$report_type': 'TestReport', 'item_index': 528, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_secondary_files_implicit + location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + when: runtest + nodeid: tests/test_provenance.py::test_secondary_files_implicit + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_provenance.py::test_secondary_files_explicit + location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.003713201000209665, 'start': 1685951465.804359, 'stop': 1685951465.808074, '$report_type': 'TestReport', 'item_index': 642, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_leave_tmpdirs', 'location': ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs'), 'keywords': {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env4.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env4.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env4.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env4.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env4.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python3"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "env0.py"\n }\n]\nDEBUG cwltool:job.py:215 [job env4.cwl] initial work dir {\n "_:71d3e5f1-6a63-4f12-8e4e-da560d54b9f0": [\n "import os\\nfor k, v in os.environ.items():\\n print(f\\"{k}={v}\\", end=\\"\\\\0\\")\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/env0.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job env4.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj$ python3 \\\n env0.py > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env4.cwl] completed success\nDEBUG cwltool:job.py:422 [job env4.cwl] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b",\n "basename": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameroot": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6da6366e8e172fcac257989bcfedf15da64e9a2a",\n "size": 1261,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/out/062565172eb482b02386f50adec0303a9a80c77b\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.8227042449998407, 'start': 1685951464.986022, 'stop': 1685951465.8087091, '$report_type': 'TestReport', 'item_index': 637, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_leave_tmpdirs', 'location': ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs'), 'keywords': {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env4.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env4.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env4.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env4.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env4.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python3"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "env0.py"\n }\n]\nDEBUG cwltool:job.py:215 [job env4.cwl] initial work dir {\n "_:71d3e5f1-6a63-4f12-8e4e-da560d54b9f0": [\n "import os\\nfor k, v in os.environ.items():\\n print(f\\"{k}={v}\\", end=\\"\\\\0\\")\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/env0.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job env4.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj$ python3 \\\n env0.py > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env4.cwl] completed success\nDEBUG cwltool:job.py:422 [job env4.cwl] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b",\n "basename": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameroot": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6da6366e8e172fcac257989bcfedf15da64e9a2a",\n "size": 1261,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/out/062565172eb482b02386f50adec0303a9a80c77b\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.019946255999457208, 'start': 1685951465.809982, 'stop': 1685951465.82993, '$report_type': 'TestReport', 'item_index': 637, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_explicit', 'location': ('tests/test_provenance.py', 119, 'test_secondary_files_explicit'), 'keywords': {'test_secondary_files_explicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.022172081999997317, 'start': 1685951465.808274, 'stop': 1685951465.8304498, '$report_type': 'TestReport', 'item_index': 529, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_tmpdir.py::test_leave_tmpdirs + location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0019066180002482724, 'start': 1685951465.833351, 'stop': 1685951465.835259, '$report_type': 'TestReport', 'item_index': 640, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_target.py::test_wrong_target', 'location': ('tests/test_target.py', 12, 'test_wrong_target'), 'keywords': {'test_wrong_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mI'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\nERROR cwltool:main.py:1218 I'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'")], 'duration': 1.5277158919998328, 'start': 1685951464.511601, 'stop': 1685951466.0392802, '$report_type': 'TestReport', 'item_index': 628, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_target.py::test_wrong_target', 'location': ('tests/test_target.py', 12, 'test_wrong_target'), 'keywords': {'test_wrong_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mI'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\nERROR cwltool:main.py:1218 I'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'")], 'duration': 0.00023238100038724951, 'start': 1685951466.039777, 'stop': 1685951466.040011, '$report_type': 'TestReport', 'item_index': 628, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_target.py::test_wrong_target + location: ('tests/test_target.py', 12, 'test_wrong_target') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]'), 'keywords': {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0021708399999624817, 'start': 1685951466.04311, 'stop': 1685951466.0452821, '$report_type': 'TestReport', 'item_index': 638, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_target.py::test_target_packed', 'location': ('tests/test_target.py', 29, 'test_target_packed'), 'keywords': {'test_target_packed': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#echo as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmp4ub_5xg8\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpqn2zozpb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxsls6qw3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplfi3vkzu\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.532981734000714, 'start': 1685951464.525578, 'stop': 1685951466.0585248, '$report_type': 'TestReport', 'item_index': 629, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_target.py::test_target_packed', 'location': ('tests/test_target.py', 29, 'test_target_packed'), 'keywords': {'test_target_packed': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#echo as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmp4ub_5xg8\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpqn2zozpb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxsls6qw3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplfi3vkzu\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0004789479999089963, 'start': 1685951466.0598578, 'stop': 1685951466.060338, '$report_type': 'TestReport', 'item_index': 629, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_target.py::test_target_packed + location: ('tests/test_target.py', 29, 'test_target_packed') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]'), 'keywords': {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.002468566999596078, 'start': 1685951466.062423, 'stop': 1685951466.064893, '$report_type': 'TestReport', 'item_index': 639, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script\n [-h] --foo.one FOO.ONE --foo.two FOO.TWO [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --foo.one FOO.ONE\n --foo.two FOO.TWO\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'")], 'duration': 0.6442673579995244, 'start': 1685951465.835901, 'stop': 1685951466.480154, '$report_type': 'TestReport', 'item_index': 640, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script\n [-h] --foo.one FOO.ONE --foo.two FOO.TWO [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --foo.one FOO.ONE\n --foo.two FOO.TWO\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'")], 'duration': 0.00038592599958064966, 'start': 1685951466.4809642, 'stop': 1685951466.481351, '$report_type': 'TestReport', 'item_index': 640, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparser_with_doc + location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_with_doc', 'location': ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc'), 'keywords': {'test_argparser_with_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002025419998972211, 'start': 1685951466.483218, 'stop': 1685951466.4834208, '$report_type': 'TestReport', 'item_index': 645, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_with_doc', 'location': ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc'), 'keywords': {'test_argparser_with_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'")], 'duration': 0.011666497999613057, 'start': 1685951466.483816, 'stop': 1685951466.4954839, '$report_type': 'TestReport', 'item_index': 645, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_with_doc', 'location': ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc'), 'keywords': {'test_argparser_with_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'")], 'duration': 0.0002207099996667239, 'start': 1685951466.496104, 'stop': 1685951466.496326, '$report_type': 'TestReport', 'item_index': 645, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparser_with_doc + location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1]', 'location': ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]'), 'keywords': {'test_argparse_append_with_default[job_order1-expected_values1]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order1-expected_values1': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005410029998529353, 'start': 1685951466.498595, 'stop': 1685951466.499137, '$report_type': 'TestReport', 'item_index': 648, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '"cymbal2"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpqi4cps3i\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqi4cps3i\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.714671594999345, 'start': 1685951465.808789, 'stop': 1685951466.523444, '$report_type': 'TestReport', 'item_index': 642, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '"cymbal2"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpqi4cps3i\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqi4cps3i\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000832688000627968, 'start': 1685951466.5242019, 'stop': 1685951466.525036, '$report_type': 'TestReport', 'item_index': 642, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0017929050000020652, 'start': 1685951466.527004, 'stop': 1685951466.5287979, '$report_type': 'TestReport', 'item_index': 643, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]'), 'keywords': {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjo7d5ug0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_9] initial work dir {}\nINFO cwltool:job.py:266 [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_9] completed success\nDEBUG cwltool:job.py:422 [job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\nDEBUG cwltool:job.py:454 [job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjo7d5ug0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6606748949998291, 'start': 1685951466.046178, 'stop': 1685951466.70684, '$report_type': 'TestReport', 'item_index': 638, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]'), 'keywords': {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script\n [-h] --bdg [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --bdg\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'")], 'duration': 0.6429743959997722, 'start': 1685951466.065346, 'stop': 1685951466.7083058, '$report_type': 'TestReport', 'item_index': 639, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]'), 'keywords': {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjo7d5ug0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_9] initial work dir {}\nINFO cwltool:job.py:266 [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_9] completed success\nDEBUG cwltool:job.py:422 [job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\nDEBUG cwltool:job.py:454 [job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjo7d5ug0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0010807290000229841, 'start': 1685951466.7084632, 'stop': 1685951466.709545, '$report_type': 'TestReport', 'item_index': 638, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]'), 'keywords': {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script\n [-h] --bdg [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --bdg\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'")], 'duration': 0.00043712600017897785, 'start': 1685951466.709005, 'stop': 1685951466.709443, '$report_type': 'TestReport', 'item_index': 639, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='teardown' outcome='passed'> [hook] + finish pytest_report_from_serializable --> ]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_argparser_without_doc + location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0]', 'location': ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]'), 'keywords': {'test_argparse_append_with_default[job_order0-expected_values0]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order0-expected_values0': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005423120001069037, 'start': 1685951466.713546, 'stop': 1685951466.7140899, '$report_type': 'TestReport', 'item_index': 647, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_without_doc', 'location': ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc'), 'keywords': {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00038347800000337884, 'start': 1685951466.7141151, 'stop': 1685951466.7145011, '$report_type': 'TestReport', 'item_index': 646, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_without_doc', 'location': ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc'), 'keywords': {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'")], 'duration': 0.019146607000038784, 'start': 1685951466.715123, 'stop': 1685951466.734271, '$report_type': 'TestReport', 'item_index': 646, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_without_doc', 'location': ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc'), 'keywords': {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'")], 'duration': 0.00028543000007630326, 'start': 1685951466.734833, 'stop': 1685951466.7351198, '$report_type': 'TestReport', 'item_index': 646, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparser_without_doc + location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_udocker.py::test_udocker_usage_should_not_write_cid_file + location: ('tests/test_udocker.py', 45, 'test_udocker_usage_should_not_write_cid_file') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_udocker.py::test_udocker_usage_should_not_write_cid_file', 'location': ('tests/test_udocker.py', 45, 'test_udocker_usage_should_not_write_cid_file'), 'keywords': {'test_udocker_usage_should_not_write_cid_file': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_udocker.py', 46, 'Skipped: LINUX only'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003216280001652194, 'start': 1685951466.737472, 'stop': 1685951466.737795, '$report_type': 'TestReport', 'item_index': 652, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_udocker.py::test_udocker_usage_should_not_write_cid_file', 'location': ('tests/test_udocker.py', 45, 'test_udocker_usage_should_not_write_cid_file'), 'keywords': {'test_udocker_usage_should_not_write_cid_file': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00022743400040781125, 'start': 1685951466.738656, 'stop': 1685951466.7388852, '$report_type': 'TestReport', 'item_index': 652, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_udocker.py::test_udocker_usage_should_not_write_cid_file + location: ('tests/test_udocker.py', 45, 'test_udocker_usage_should_not_write_cid_file') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_udocker.py::test_udocker_should_display_memory_usage + location: ('tests/test_udocker.py', 69, 'test_udocker_should_display_memory_usage') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_udocker.py::test_udocker_should_display_memory_usage', 'location': ('tests/test_udocker.py', 69, 'test_udocker_should_display_memory_usage'), 'keywords': {'test_udocker_should_display_memory_usage': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_udocker.py', 70, 'Skipped: Linux only'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002621650000946829, 'start': 1685951466.741861, 'stop': 1685951466.742125, '$report_type': 'TestReport', 'item_index': 653, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_udocker.py::test_udocker_should_display_memory_usage', 'location': ('tests/test_udocker.py', 69, 'test_udocker_should_display_memory_usage'), 'keywords': {'test_udocker_should_display_memory_usage': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00019226799940952333, 'start': 1685951466.7427552, 'stop': 1685951466.742949, '$report_type': 'TestReport', 'item_index': 653, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_udocker.py::test_udocker_should_display_memory_usage + location: ('tests/test_udocker.py', 69, 'test_udocker_should_display_memory_usage') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_udocker.py::test_udocker_nobanner + location: ('tests/test_udocker.py', 91, 'test_udocker_nobanner') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_udocker.py::test_udocker_nobanner', 'location': ('tests/test_udocker.py', 91, 'test_udocker_nobanner'), 'keywords': {'test_udocker_nobanner': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_udocker.py', 92, 'Skipped: LINUX only'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00024224099979619496, 'start': 1685951466.7450528, 'stop': 1685951466.745297, '$report_type': 'TestReport', 'item_index': 654, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_udocker.py::test_udocker_nobanner', 'location': ('tests/test_udocker.py', 91, 'test_udocker_nobanner'), 'keywords': {'test_udocker_nobanner': 1, 'skipif': 1, 'pytestmark': 1, 'test_udocker.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002610439996715286, 'start': 1685951466.7458901, 'stop': 1685951466.746152, '$report_type': 'TestReport', 'item_index': 654, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_udocker.py::test_udocker_nobanner + location: ('tests/test_udocker.py', 91, 'test_udocker_nobanner') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_validate.py::test_validate_graph_with_no_default + location: ('tests/test_validate.py', 6, 'test_validate_graph_with_no_default') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate.py::test_validate_graph_with_no_default', 'location': ('tests/test_validate.py', 6, 'test_validate_graph_with_no_default'), 'keywords': {'test_validate_graph_with_no_default': 1, 'test_validate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003242369994040928, 'start': 1685951466.7482119, 'stop': 1685951466.748538, '$report_type': 'TestReport', 'item_index': 655, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_explicit', 'location': ('tests/test_provenance.py', 119, 'test_secondary_files_explicit'), 'keywords': {'test_secondary_files_explicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\n\x1b[1;30mINFO\x1b[0m [workflow _20] start\n\x1b[1;30mINFO\x1b[0m [workflow _20] starting step step1_4\n\x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[1;30mINFO\x1b[0m [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\n\x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _20] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to 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\'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ab5d55af482cae1b1829c3da3ee604ee1fb46e6c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: e16b2b9f3a4ea3c4db3ad2bb71e39cdd02c1fde2a446528a68596c88de6ce0ad workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0173fb349bad74105b30c7b54ebfc79bc650689ee08d2810530ae536a1b064eaf25c7b9f15d9c9dfd3e685437e64a2e8d5c55dd9ac21dae1ac0ee2dc95b3c641 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmp9gj9l2fa\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp46c_retm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5ft4gx95\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp96w7gil\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 509e405f0bd8ef93211df57e39be176d12666adc metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 262ec7432d66db0b5ed1cd59aa1af4cd4be1124dbc4af94e86bb6b512289b670 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0119a8de57eb87221919bb6f241bdbe06282b70055adb1d5ae33b9c6f69d081928b3f227305cef219b208ab543d013f5244e55ec7b86517988eaed08f44786f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 45b1c340c57cf230ed17b4e630abdf1efade240e metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: eb6898093916925d311c393e4d05c7526bb1cc611d0dde25b34dd9e93b53bbc4 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 3bf0f3cd885ac1a11daa3a4ddd0c2a1629c6ca2c4ebbb55721070a7aab577a15e431939a7983d567fdfc52b7c6cd4ac9cc7301dc550254a3f5c54bc614f33337 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 38e4d26d88163d39f1f79746d91c385a30ee9225 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0541fdfe699859ca640f637778cffea97fd5bb4b10fae765cca532bb51594598 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: dd848f7099d65e87f01861744621b13563715b0af772ac3f9c254aaf22da244075483bb03cd153771798371887f6435b579e557f5fc8e0b55abcbd63d11b3671 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0a9161af759436c0940176a0ee92ac46d033a8d2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d975c4b3006cb518b3712877f983b68a2f38e2860b23bbda21d4d5c6bc82482d metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: af800227b8ede5af124ae87add535d60d7565a31b2e0923532a6442d21e755820ef1dee20d54db2aae2585bbdc1f1d566b1a76a4d251b80d6183146da3b14b9c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 6f16628a75ecb5bc263b08aa80b2b04c289f6b85 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d7a309d015efc43f7c0d10319bd7866a9e569b1ceb945c129bfc0108f1baeeb7 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 60585141255cb9b43faafbfa26e49d21ddaeff3718becc211fc229d7b9dc2201ae89245239fc3ff9e03726bd8d99faa864df8eb661810117fb2a43f868188cb3 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0077decebf928c4d8aebf6cd1b9c40ae95443eb6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ccfe9486f117718bb534393411f3535d23abe939688867cd7fb7666948a96040 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 5f7ed9ffdc499c78afe431fa0d3ed7bd2942590ddb4cdb42b728daae7644af1f50f352669a364b61880354e56de96674c7b9faa918f33ebd112dc80f3194aa5a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ecdb0d529e82bcfae2510df67a6c624ec91cb4eb metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: f3498f65cdd7f44b2f46cdc5f8a6630bd922452b6bed63648fd8a0b0636b53e9 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 140511736f43c0e44321a2d677bb2e54684fa8e564d650558381799123517ea7a27402ecf6c826c0651360dbc351f4903847f1dc7552ecbc7bc5f372963395f7 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b73fda4904dd1bea80c96c9fc89e49aabbd83fff metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 9f14d52b82857ac1b7a45eb1bf0f6ee22105533f54c1af788fec3744102e8d97 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: b5c96592dbe7dd23e27053f734d227f91c089e42395a9a812dc4994fce5850b58c7ae04d804f92a0041ed0487a26a4e0011cd626bcd86621ae9cd773d631daae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: a28a0bc657b6e1797cdbfe4343a9adfad7fbc539 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: b32be96d6dc9f72b299be94d867dd45f884d5e0f5c416b98f8f03e691ddecec3 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 6145e7ae857af5949152de4f2773425ea722b736616597d7c4766ad6b85b57435c37240b545b770e500e565af57ba9ae25b498dfaa8c31003b65f066cfb9a62b bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance')], 'duration': 1.0753109860006589, 'start': 1685951465.8310468, 'stop': 1685951466.9063349, '$report_type': 'TestReport', 'item_index': 529, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_explicit', 'location': ('tests/test_provenance.py', 119, 'test_secondary_files_explicit'), 'keywords': {'test_secondary_files_explicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\n\x1b[1;30mINFO\x1b[0m [workflow _20] start\n\x1b[1;30mINFO\x1b[0m [workflow _20] starting step step1_4\n\x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[1;30mINFO\x1b[0m [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\n\x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _20] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ab5d55af482cae1b1829c3da3ee604ee1fb46e6c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: e16b2b9f3a4ea3c4db3ad2bb71e39cdd02c1fde2a446528a68596c88de6ce0ad workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0173fb349bad74105b30c7b54ebfc79bc650689ee08d2810530ae536a1b064eaf25c7b9f15d9c9dfd3e685437e64a2e8d5c55dd9ac21dae1ac0ee2dc95b3c641 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmp9gj9l2fa\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp46c_retm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5ft4gx95\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp96w7gil\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 509e405f0bd8ef93211df57e39be176d12666adc metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 262ec7432d66db0b5ed1cd59aa1af4cd4be1124dbc4af94e86bb6b512289b670 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0119a8de57eb87221919bb6f241bdbe06282b70055adb1d5ae33b9c6f69d081928b3f227305cef219b208ab543d013f5244e55ec7b86517988eaed08f44786f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 45b1c340c57cf230ed17b4e630abdf1efade240e metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: eb6898093916925d311c393e4d05c7526bb1cc611d0dde25b34dd9e93b53bbc4 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 3bf0f3cd885ac1a11daa3a4ddd0c2a1629c6ca2c4ebbb55721070a7aab577a15e431939a7983d567fdfc52b7c6cd4ac9cc7301dc550254a3f5c54bc614f33337 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 38e4d26d88163d39f1f79746d91c385a30ee9225 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0541fdfe699859ca640f637778cffea97fd5bb4b10fae765cca532bb51594598 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: dd848f7099d65e87f01861744621b13563715b0af772ac3f9c254aaf22da244075483bb03cd153771798371887f6435b579e557f5fc8e0b55abcbd63d11b3671 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0a9161af759436c0940176a0ee92ac46d033a8d2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d975c4b3006cb518b3712877f983b68a2f38e2860b23bbda21d4d5c6bc82482d metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: af800227b8ede5af124ae87add535d60d7565a31b2e0923532a6442d21e755820ef1dee20d54db2aae2585bbdc1f1d566b1a76a4d251b80d6183146da3b14b9c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 6f16628a75ecb5bc263b08aa80b2b04c289f6b85 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d7a309d015efc43f7c0d10319bd7866a9e569b1ceb945c129bfc0108f1baeeb7 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 60585141255cb9b43faafbfa26e49d21ddaeff3718becc211fc229d7b9dc2201ae89245239fc3ff9e03726bd8d99faa864df8eb661810117fb2a43f868188cb3 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0077decebf928c4d8aebf6cd1b9c40ae95443eb6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ccfe9486f117718bb534393411f3535d23abe939688867cd7fb7666948a96040 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 5f7ed9ffdc499c78afe431fa0d3ed7bd2942590ddb4cdb42b728daae7644af1f50f352669a364b61880354e56de96674c7b9faa918f33ebd112dc80f3194aa5a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ecdb0d529e82bcfae2510df67a6c624ec91cb4eb metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: f3498f65cdd7f44b2f46cdc5f8a6630bd922452b6bed63648fd8a0b0636b53e9 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 140511736f43c0e44321a2d677bb2e54684fa8e564d650558381799123517ea7a27402ecf6c826c0651360dbc351f4903847f1dc7552ecbc7bc5f372963395f7 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b73fda4904dd1bea80c96c9fc89e49aabbd83fff metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 9f14d52b82857ac1b7a45eb1bf0f6ee22105533f54c1af788fec3744102e8d97 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: b5c96592dbe7dd23e27053f734d227f91c089e42395a9a812dc4994fce5850b58c7ae04d804f92a0041ed0487a26a4e0011cd626bcd86621ae9cd773d631daae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: a28a0bc657b6e1797cdbfe4343a9adfad7fbc539 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: b32be96d6dc9f72b299be94d867dd45f884d5e0f5c416b98f8f03e691ddecec3 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 6145e7ae857af5949152de4f2773425ea722b736616597d7c4766ad6b85b57435c37240b545b770e500e565af57ba9ae25b498dfaa8c31003b65f066cfb9a62b bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance')], 'duration': 0.0012781379991793074, 'start': 1685951466.908513, 'stop': 1685951466.9097931, '$report_type': 'TestReport', 'item_index': 529, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_provenance.py::test_secondary_files_explicit + location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') + finish pytest_runtest_logfinish --> [] [hook] + pytest_warning_recorded [hook] + warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} + when: runtest + nodeid: tests/test_provenance.py::test_secondary_files_explicit + location: None + finish pytest_warning_recorded --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_toolargparse.py::test_dont_require_inputs + location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_dont_require_inputs', 'location': ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs'), 'keywords': {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014646170002379222, 'start': 1685951466.91312, 'stop': 1685951466.914585, '$report_type': 'TestReport', 'item_index': 644, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '"{\\"bar\\": http://example.com}"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjyzejhiw\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjyzejhiw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7014808530002483, 'start': 1685951466.5291898, 'stop': 1685951467.230655, '$report_type': 'TestReport', 'item_index': 643, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '"{\\"bar\\": http://example.com}"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjyzejhiw\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjyzejhiw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005410029998529353, 'start': 1685951467.23134, 'stop': 1685951467.231882, '$report_type': 'TestReport', 'item_index': 643, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> ]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: ]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: ]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] + location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_trs.py::test_tool_trs_template + location: ('tests/test_trs.py', 93, 'test_tool_trs_template') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_trs.py::test_tool_trs_template', 'location': ('tests/test_trs.py', 93, 'test_tool_trs_template'), 'keywords': {'test_tool_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00025567400007275864, 'start': 1685951467.234224, 'stop': 1685951467.2344801, '$report_type': 'TestReport', 'item_index': 650, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1]', 'location': ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]'), 'keywords': {'test_argparse_append_with_default[job_order1-expected_values1]': 1, 'parametrize': 1, 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<_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1]', 'location': ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]'), 'keywords': {'test_argparse_append_with_default[job_order1-expected_values1]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order1-expected_values1': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 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'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")], 'duration': 0.0003022480004801764, 'start': 1685951467.365503, 'stop': 1685951467.365806, '$report_type': 'TestReport', 'item_index': 649, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order2-expected_values2] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order2-expected_values2]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js + location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_reports_invalid_js', 'location': ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js'), 'keywords': {'test_js_hint_reports_invalid_js': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00031787399984750664, 'start': 1685951467.368246, 'stop': 1685951467.368565, '$report_type': 'TestReport', 'item_index': 659, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_reports_invalid_js', 'location': ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js'), 'keywords': {'test_js_hint_reports_invalid_js': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.013302664000548248, 'start': 1685951467.369011, 'stop': 1685951467.382315, '$report_type': 'TestReport', 'item_index': 659, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_reports_invalid_js', 'location': ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js'), 'keywords': {'test_js_hint_reports_invalid_js': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002095480003845296, 'start': 1685951467.3827882, 'stop': 1685951467.3830001, '$report_type': 'TestReport', 'item_index': 659, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js + location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_js_hint_warn_on_es6 + location: ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_warn_on_es6', 'location': ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6'), 'keywords': {'test_js_hint_warn_on_es6': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002407930005574599, 'start': 1685951467.385212, 'stop': 1685951467.3854542, '$report_type': 'TestReport', 'item_index': 660, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_warn_on_es6', 'location': ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6'), 'keywords': {'test_js_hint_warn_on_es6': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.008448042999589234, 'start': 1685951467.386027, 'stop': 1685951467.394476, '$report_type': 'TestReport', 'item_index': 660, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_warn_on_es6', 'location': ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6'), 'keywords': {'test_js_hint_warn_on_es6': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002241669999420992, 'start': 1685951467.395021, 'stop': 1685951467.3952472, '$report_type': 'TestReport', 'item_index': 660, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_js_hint_warn_on_es6 + location: ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_js_hint_error_on_undefined_name + location: ('tests/test_validate_js.py', 74, 'test_js_hint_error_on_undefined_name') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_error_on_undefined_name', 'location': ('tests/test_validate_js.py', 74, 'test_js_hint_error_on_undefined_name'), 'keywords': {'test_js_hint_error_on_undefined_name': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00031343499995273305, 'start': 1685951467.397362, 'stop': 1685951467.397677, '$report_type': 'TestReport', 'item_index': 661, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_error_on_undefined_name', 'location': ('tests/test_validate_js.py', 74, 'test_js_hint_error_on_undefined_name'), 'keywords': {'test_js_hint_error_on_undefined_name': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.010393013000793871, 'start': 1685951467.398325, 'stop': 1685951467.4087198, '$report_type': 'TestReport', 'item_index': 661, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_error_on_undefined_name', 'location': ('tests/test_validate_js.py', 74, 'test_js_hint_error_on_undefined_name'), 'keywords': {'test_js_hint_error_on_undefined_name': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00035033899985137396, 'start': 1685951467.4096682, 'stop': 1685951467.41002, '$report_type': 'TestReport', 'item_index': 661, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport 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'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003560980003385339, 'start': 1685951467.4127629, 'stop': 1685951467.413121, '$report_type': 'TestReport', 'item_index': 662, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_set_defined_name', 'location': ('tests/test_validate_js.py', 78, 'test_js_hint_set_defined_name'), 'keywords': {'test_js_hint_set_defined_name': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.006926598000063677, 'start': 1685951467.413738, 'stop': 1685951467.4206662, '$report_type': 'TestReport', 'item_index': 662, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_set_defined_name', 'location': ('tests/test_validate_js.py', 78, 'test_js_hint_set_defined_name'), 'keywords': {'test_js_hint_set_defined_name': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00020684699939010898, 'start': 1685951467.421165, 'stop': 1685951467.421373, '$report_type': 'TestReport', 'item_index': 662, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_js_hint_set_defined_name + location: ('tests/test_validate_js.py', 78, 'test_js_hint_set_defined_name') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_windows_warning.py::test_windows_warning + location: ('tests/test_windows_warning.py', 12, 'test_windows_warning') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_windows_warning.py::test_windows_warning', 'location': ('tests/test_windows_warning.py', 12, 'test_windows_warning'), 'keywords': {'test_windows_warning': 1, 'test_windows_warning.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007037330005914555, 'start': 1685951467.4243672, 'stop': 1685951467.425073, '$report_type': 'TestReport', 'item_index': 663, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_windows_warning.py::test_windows_warning', 'location': ('tests/test_windows_warning.py', 12, 'test_windows_warning'), 'keywords': {'test_windows_warning': 1, 'test_windows_warning.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006785279992982396, 'start': 1685951467.4255328, 'stop': 1685951467.426213, '$report_type': 'TestReport', 'item_index': 663, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_windows_warning.py::test_windows_warning', 'location': ('tests/test_windows_warning.py', 12, 'test_windows_warning'), 'keywords': {'test_windows_warning': 1, 'test_windows_warning.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.004307549000259314, 'start': 1685951467.426868, 'stop': 1685951467.431178, '$report_type': 'TestReport', 'item_index': 663, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_windows_warning.py::test_windows_warning + location: ('tests/test_windows_warning.py', 12, 'test_windows_warning') + finish pytest_runtest_logfinish --> [] [hook] + pytest_testnodedown [hook] + node: + error: None + finish pytest_testnodedown --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0]', 'location': ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]'), 'keywords': {'test_argparse_append_with_default[job_order0-expected_values0]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order0-expected_values0': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")], 'duration': 0.9063059879999855, 'start': 1685951466.7145128, 'stop': 1685951467.6207979, '$report_type': 'TestReport', 'item_index': 647, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0]', 'location': ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]'), 'keywords': {'test_argparse_append_with_default[job_order0-expected_values0]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order0-expected_values0': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")], 'duration': 0.00041723600043042097, 'start': 1685951467.621684, 'stop': 1685951467.622103, '$report_type': 'TestReport', 'item_index': 647, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] + location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_trs.py::test_workflow_trs_template + location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_trs.py::test_workflow_trs_template', 'location': ('tests/test_trs.py', 107, 'test_workflow_trs_template'), 'keywords': {'test_workflow_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004815839993170812, 'start': 1685951467.624228, 'stop': 1685951467.624712, '$report_type': 'TestReport', 'item_index': 651, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate.py::test_validate_graph_with_no_default', 'location': ('tests/test_validate.py', 6, 'test_validate_graph_with_no_default'), 'keywords': {'test_validate_graph_with_no_default': 1, 'test_validate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl'\nWARNING root:main.py:1124 File contains $graph of multiple objects and no default process (#main). Validating all objects:")], 'duration': 0.9934901919996264, 'start': 1685951466.7491899, 'stop': 1685951467.742657, '$report_type': 'TestReport', 'item_index': 655, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate.py::test_validate_graph_with_no_default', 'location': ('tests/test_validate.py', 6, 'test_validate_graph_with_no_default'), 'keywords': {'test_validate_graph_with_no_default': 1, 'test_validate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl'\nWARNING root:main.py:1124 File contains $graph of multiple objects and no default process (#main). Validating all objects:")], 'duration': 0.00020839900025748648, 'start': 1685951467.743108, 'stop': 1685951467.743317, '$report_type': 'TestReport', 'item_index': 655, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate.py::test_validate_graph_with_no_default + location: ('tests/test_validate.py', 6, 'test_validate_graph_with_no_default') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_get_expressions + location: ('tests/test_validate_js.py', 24, 'test_get_expressions') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_get_expressions', 'location': ('tests/test_validate_js.py', 24, 'test_get_expressions'), 'keywords': {'test_get_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00021349599956010934, 'start': 1685951467.7448692, 'stop': 1685951467.7450838, '$report_type': 'TestReport', 'item_index': 656, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_with_step_level_default_value', 'location': ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value'), 'keywords': {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', 'latest: Pulling from library/alpine\nDigest: sha256:02bb6f428431fbc2809c5d1b41eab5a68350194fb508869a33cb1af4444c9b11\nStatus: Image is up to date for alpine:latest\ndocker.io/library/alpine:latest\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:argparser.py:943 Can\'t make command line argument from Any\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "message": "two"\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step task2\nDEBUG cwltool:workflow_job.py:727 [step task2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2] start\nDEBUG cwltool:command_line_tool.py:982 [job task2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2\nDEBUG cwltool:command_line_tool.py:988 [job task2] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/alpine:latest\']\nDEBUG cwltool:job.py:215 [job task2] initial work dir {}\nINFO cwltool:job.py:266 [job task2] /private/tmp/docker_tmp2vpjz9j3$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2vpjz9j3,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpbyyklcxx,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpwtgdio32/20230605095106-754192.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2] completed success\nDEBUG cwltool:job.py:422 [job task2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2vpjz9j3/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {}\nDEBUG cwltool:job.py:446 [job task2] Removing input staging directory /private/tmp/docker_tmpy2a25zaq\nDEBUG cwltool:job.py:454 [job task2] Removing temporary directory /private/tmp/docker_tmpbyyklcxx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2vpjz9j3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpysive81g\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 4.140258484999322, 'start': 1685951463.636079, 'stop': 1685951467.776237, '$report_type': 'TestReport', 'item_index': 623, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_subgraph.py::test_single_with_step_level_default_value', 'location': ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value'), 'keywords': {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', 'latest: Pulling from library/alpine\nDigest: sha256:02bb6f428431fbc2809c5d1b41eab5a68350194fb508869a33cb1af4444c9b11\nStatus: Image is up to date for alpine:latest\ndocker.io/library/alpine:latest\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:argparser.py:943 Can\'t make command line argument from Any\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "message": "two"\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step task2\nDEBUG cwltool:workflow_job.py:727 [step task2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2] start\nDEBUG cwltool:command_line_tool.py:982 [job task2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2\nDEBUG cwltool:command_line_tool.py:988 [job task2] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/alpine:latest\']\nDEBUG cwltool:job.py:215 [job task2] initial work dir {}\nINFO cwltool:job.py:266 [job task2] /private/tmp/docker_tmp2vpjz9j3$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2vpjz9j3,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpbyyklcxx,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpwtgdio32/20230605095106-754192.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2] completed success\nDEBUG cwltool:job.py:422 [job task2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2vpjz9j3/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {}\nDEBUG cwltool:job.py:446 [job task2] Removing input staging directory /private/tmp/docker_tmpy2a25zaq\nDEBUG cwltool:job.py:454 [job task2] Removing temporary directory /private/tmp/docker_tmpbyyklcxx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2vpjz9j3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpysive81g\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00046557099994970486, 'start': 1685951467.777664, 'stop': 1685951467.778131, '$report_type': 'TestReport', 'item_index': 623, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value + location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix + location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix'), 'keywords': {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.002130539000063436, 'start': 1685951467.780889, 'stop': 1685951467.783021, '$report_type': 'TestReport', 'item_index': 632, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix'), 'keywords': {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']\n"), ('Captured log call', "INFO cwltool:docker.py:164 ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']")], 'duration': 0.09524703099941689, 'start': 1685951467.7836092, 'stop': 1685951467.878856, '$report_type': 'TestReport', 'item_index': 632, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix'), 'keywords': {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']\n"), ('Captured log call', "INFO cwltool:docker.py:164 ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']")], 'duration': 0.003588997999941057, 'start': 1685951467.880084, 'stop': 1685951467.8836741, '$report_type': 'TestReport', 'item_index': 632, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix + location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') + finish pytest_runtest_logfinish --> [] [hook] + pytest_testnodedown [hook] + node: + error: None + finish pytest_testnodedown --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_trs.py::test_tool_trs_template', 'location': ('tests/test_trs.py', 93, 'test_tool_trs_template'), 'keywords': {'test_tool_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\nINFO cwltool:load_tool.py:102 Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'")], 'duration': 0.6917008549999082, 'start': 1685951467.234879, 'stop': 1685951467.9265652, '$report_type': 'TestReport', 'item_index': 650, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_trs.py::test_tool_trs_template', 'location': ('tests/test_trs.py', 93, 'test_tool_trs_template'), 'keywords': {'test_tool_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\nINFO cwltool:load_tool.py:102 Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'")], 'duration': 0.00021415700030047446, 'start': 1685951467.9271948, 'stop': 1685951467.92741, '$report_type': 'TestReport', 'item_index': 650, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_trs.py::test_tool_trs_template + location: ('tests/test_trs.py', 93, 'test_tool_trs_template') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_js_hint_basic + location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_basic', 'location': ('tests/test_validate_js.py', 53, 'test_js_hint_basic'), 'keywords': {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002251839996461058, 'start': 1685951467.929321, 'stop': 1685951467.929547, '$report_type': 'TestReport', 'item_index': 658, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_basic', 'location': ('tests/test_validate_js.py', 53, 'test_js_hint_basic'), 'keywords': {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.010393084999122948, 'start': 1685951467.930013, 'stop': 1685951467.940408, '$report_type': 'TestReport', 'item_index': 658, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_basic', 'location': ('tests/test_validate_js.py', 53, 'test_js_hint_basic'), 'keywords': {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0015349340001193923, 'start': 1685951467.940873, 'stop': 1685951467.942409, '$report_type': 'TestReport', 'item_index': 658, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_js_hint_basic + location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') + finish pytest_runtest_logfinish --> [] [hook] + pytest_testnodedown [hook] + node: + error: None + finish pytest_testnodedown --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_trs.py::test_workflow_trs_template', 'location': ('tests/test_trs.py', 107, 'test_workflow_trs_template'), 'keywords': {'test_workflow_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\nINFO cwltool:load_tool.py:102 Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'")], 'duration': 0.6574194070008161, 'start': 1685951467.625265, 'stop': 1685951468.282669, '$report_type': 'TestReport', 'item_index': 651, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_trs.py::test_workflow_trs_template', 'location': ('tests/test_trs.py', 107, 'test_workflow_trs_template'), 'keywords': {'test_workflow_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\nINFO cwltool:load_tool.py:102 Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'")], 'duration': 0.0025651939995441353, 'start': 1685951468.283201, 'stop': 1685951468.285768, '$report_type': 'TestReport', 'item_index': 651, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_trs.py::test_workflow_trs_template + location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') + finish pytest_runtest_logfinish --> [] [hook] + pytest_testnodedown [hook] + node: + error: None + finish pytest_testnodedown --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_get_expressions', 'location': ('tests/test_validate_js.py', 24, 'test_get_expressions'), 'keywords': {'test_get_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.6003651379996882, 'start': 1685951467.7454169, 'stop': 1685951468.345769, '$report_type': 'TestReport', 'item_index': 656, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_get_expressions', 'location': ('tests/test_validate_js.py', 24, 'test_get_expressions'), 'keywords': {'test_get_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0020412240000950987, 'start': 1685951468.346211, 'stop': 1685951468.348253, '$report_type': 'TestReport', 'item_index': 656, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_get_expressions + location: ('tests/test_validate_js.py', 24, 'test_get_expressions') + finish pytest_runtest_logfinish --> [] [hook] + pytest_testnodedown [hook] + node: + error: None + finish pytest_testnodedown --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_dont_require_inputs', 'location': ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs'), 'keywords': {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nusage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\n [-h] --input INPUT [job_order]\n/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script: error: the following arguments are required: --input\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.982607547999578, 'start': 1685951466.914974, 'stop': 1685951468.897533, '$report_type': 'TestReport', 'item_index': 644, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_toolargparse.py::test_dont_require_inputs', 'location': ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs'), 'keywords': {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nusage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\n [-h] --input INPUT [job_order]\n/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script: error: the following arguments are required: --input\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00028186799954710295, 'start': 1685951468.898069, 'stop': 1685951468.8983521, '$report_type': 'TestReport', 'item_index': 644, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_toolargparse.py::test_dont_require_inputs + location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_validate_js.py::test_validate_js_expressions + location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_validate_js_expressions', 'location': ('tests/test_validate_js.py', 36, 'test_validate_js_expressions'), 'keywords': {'test_validate_js_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003742219996638596, 'start': 1685951468.900276, 'stop': 1685951468.900651, '$report_type': 'TestReport', 'item_index': 657, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_validate_js_expressions', 'location': ('tests/test_validate_js.py', 36, 'test_validate_js_expressions'), 'keywords': {'test_validate_js_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:08]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.\x1b[0m\n"), ('Captured log call', "WARNING cwltool:validate_js.py:208 JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.")], 'duration': 0.016739755000344303, 'start': 1685951468.9009879, 'stop': 1685951468.9177291, '$report_type': 'TestReport', 'item_index': 657, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_validate_js.py::test_validate_js_expressions', 'location': ('tests/test_validate_js.py', 36, 'test_validate_js_expressions'), 'keywords': {'test_validate_js_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:08]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.\x1b[0m\n"), ('Captured log call', "WARNING cwltool:validate_js.py:208 JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.")], 'duration': 0.0022302220004348783, 'start': 1685951468.91821, 'stop': 1685951468.920442, '$report_type': 'TestReport', 'item_index': 657, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_validate_js.py::test_validate_js_expressions + location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') + finish pytest_runtest_logfinish --> [] [hook] + pytest_testnodedown [hook] + node: + error: None + finish pytest_testnodedown --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_schemadef.py::test_schemadef', 'location': ('tests/test_schemadef.py', 7, 'test_schemadef'), 'keywords': {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard")], 'duration': 14.348487793000459, 'start': 1685951454.6698, 'stop': 1685951469.017929, '$report_type': 'TestReport', 'item_index': 578, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_schemadef.py::test_schemadef', 'location': ('tests/test_schemadef.py', 7, 'test_schemadef'), 'keywords': {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard")], 'duration': 0.0002445029995215009, 'start': 1685951469.018733, 'stop': 1685951469.018979, '$report_type': 'TestReport', 'item_index': 578, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_schemadef.py::test_schemadef + location: ('tests/test_schemadef.py', 7, 'test_schemadef') + finish pytest_runtest_logfinish --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_obscuring', 'location': ('tests/test_secrets.py', 24, 'test_obscuring'), 'keywords': {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003606910004236852, 'start': 1685951469.0202398, 'stop': 1685951469.020601, '$report_type': 'TestReport', 'item_index': 579, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_obscuring', 'location': ('tests/test_secrets.py', 24, 'test_obscuring'), 'keywords': {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00022766500023863045, 'start': 1685951469.020917, 'stop': 1685951469.021145, '$report_type': 'TestReport', 'item_index': 579, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_obscuring', 'location': ('tests/test_secrets.py', 24, 'test_obscuring'), 'keywords': {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00021421099972940283, 'start': 1685951469.021472, 'stop': 1685951469.021687, '$report_type': 'TestReport', 'item_index': 579, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_secrets.py::test_obscuring + location: ('tests/test_secrets.py', 24, 'test_obscuring') + finish pytest_runtest_logstart --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logreport [hook] + report: + pytest_report_teststatus [hook] + report: + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_secrets.py::test_obscuring + location: ('tests/test_secrets.py', 24, 'test_obscuring') + finish pytest_runtest_logfinish --> [] [hook] + pytest_runtest_logstart [hook] + nodeid: tests/test_secrets.py::test_secrets[-hello bar] + location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') + finish pytest_runtest_logstart --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secrets[-hello bar]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]'), 'keywords': {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005970800002614851, 'start': 1685951469.022847, 'stop': 1685951469.023445, '$report_type': 'TestReport', 'item_index': 580, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> -hello bar]' when='setup' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -hello bar]' when='setup' outcome='passed'> + pytest_report_teststatus [hook] + report: -hello bar]' when='setup' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secrets[-hello bar]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]'), 'keywords': {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002542570000514388, 'start': 1685951469.023823, 'stop': 1685951469.0240781, '$report_type': 'TestReport', 'item_index': 580, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> -hello bar]' when='call' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -hello bar]' when='call' outcome='passed'> + pytest_report_teststatus [hook] + report: -hello bar]' when='call' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_report_from_serializable [hook] + config: <_pytest.config.Config object at 0x11074ef80> + data: {'nodeid': 'tests/test_secrets.py::test_secrets[-hello bar]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]'), 'keywords': {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006589340000573429, 'start': 1685951469.0244741, 'stop': 1685951469.025135, '$report_type': 'TestReport', 'item_index': 580, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} + finish pytest_report_from_serializable --> -hello bar]' when='teardown' outcome='passed'> [hook] + pytest_runtest_logreport [hook] + report: -hello bar]' when='teardown' outcome='passed'> + pytest_report_teststatus [hook] + report: -hello bar]' when='teardown' outcome='passed'> + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_report_teststatus --> ('', '', '') [hook] + finish pytest_runtest_logreport --> [] [hook] + pytest_runtest_logfinish [hook] + nodeid: tests/test_secrets.py::test_secrets[-hello bar] + location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') + finish pytest_runtest_logfinish --> [] [hook] + pytest_testnodedown [hook] + node: + error: None + finish pytest_testnodedown --> [] [hook] + pytest_keyboard_interrupt [hook] + excinfo: + finish pytest_keyboard_interrupt --> [] [hook] + pytest_sessionfinish [hook] + session: testsfailed=6 testscollected=664> + exitstatus: 2 + finish pytest_sessionfinish --> [] [hook] + pytest_unconfigure [hook] + config: <_pytest.config.Config object at 0x11074ef80> + finish pytest_unconfigure --> [] [hook] diff --git a/tests/wf/directory_no_listing.cwl b/tests/wf/directory_no_listing.cwl new file mode 100644 index 000000000..0375baa39 --- /dev/null +++ b/tests/wf/directory_no_listing.cwl @@ -0,0 +1,79 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.2 +class: Workflow + +doc: > + Inspect provided directory and return filenames. + Generate a new directory and return it (including content). + +hints: + - class: DockerRequirement + dockerPull: docker.io/debian:stable-slim + +inputs: + dir: + type: Directory + loadListing: deep_listing + ignore: + type: Directory + loadListing: no_listing + ignore_no_info: + type: Directory + + +steps: + ls: + in: + dir: dir + ignore: ignore + out: + [listing] + run: + class: CommandLineTool + baseCommand: ls + inputs: + dir: + type: Directory + inputBinding: + position: 1 + ignore: + type: Directory + inputBinding: + position: 2 + outputs: + listing: + type: stdout + + generate: + in: [] + out: + [dir1] + run: + class: CommandLineTool + requirements: + ShellCommandRequirement: {} + LoadListingRequirement: + loadListing: deep_listing + + arguments: + - shellQuote: false + valueFrom: > + pwd; + mkdir -p dir1/a/b; + echo -n a > dir1/a.txt; + echo -n b > dir1/a/b.txt; + echo -n c > dir1/a/b/c.txt; + inputs: [] + outputs: + dir1: + type: Directory + outputBinding: + glob: "dir1" + +outputs: + output_1: + type: File + outputSource: ls/listing + output_2: + type: Directory + outputSource: generate/dir1 From ab0738f47153c58553c1656b94a92c3aef895e19 Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Mon, 12 Jun 2023 08:38:46 +0200 Subject: [PATCH 02/34] improved test case with checking if the files are there and if they are not there --- cwltool/cwlprov/provenance_profile.py | 4 +- tests/test_provenance.py | 49 +- ...nce.py::test_directory_workflow_no_listing | 32987 ---------------- 3 files changed, 26 insertions(+), 33014 deletions(-) delete mode 100644 tests/test_provenance.py::test_directory_workflow_no_listing diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index f9ff5ee9f..609d9523e 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -410,8 +410,8 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: # a later call to this method will sort that is_empty = True - if "listing" not in value: - get_listing(self.fsaccess, value) + # if "listing" not in value: + # get_listing(self.fsaccess, value) for entry in cast(MutableSequence[CWLObjectType], value.get("listing", [])): is_empty = False # Declare child-artifacts diff --git a/tests/test_provenance.py b/tests/test_provenance.py index 231da5afa..c4c23e94c 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -815,8 +815,6 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: @param tmp_path: """ - dir2 = tmp_path / "dir_deep_listing" - dir2.mkdir() sha1 = { # Expected hashes of ASCII letters (no linefeed) # as returned from: @@ -824,7 +822,22 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: "a": "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8", "b": "e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98", "c": "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4", + # Expected hashes of ASCII letters (no linefeed) + # as returned from: + # for x in d e f ; do echo -n $x | sha1sum ; done + "d": "3c363836cf4e16666669a25da280a1865c2d2874", + "e": "58e6b3a414a1e090dfc6029add0f3555ccba127f", + "f": "4a0a19218e082a343a1b17e5333409af9d98f0f5", + # Expected hashes of ASCII letters (no linefeed) + # as returned from: + # for x in g h i ; do echo -n $x | sha1sum ; done + "g": "54fd1711209fb1c0781092374132c66e79e2241b", + "h": "27d5482eebd075de44389774fce28c69f45c8a75", + "i": "042dc4512fa3d391c5170cf3aa61e6a638f84342", } + + dir2 = tmp_path / "dir_deep_listing" + dir2.mkdir() for x in "abc": # Make test files with predictable hashes with open(dir2 / x, "w", encoding="ascii") as f: @@ -832,14 +845,7 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: dir3 = tmp_path / "dir_no_listing" dir3.mkdir() - sha1 = { - # Expected hashes of ASCII letters (no linefeed) - # as returned from: - # for x in d e f ; do echo -n $x | sha1sum ; done - "d": "3c363836cf4e16666669a25da280a1865c2d2874", - "e": "58e6b3a414a1e090dfc6029add0f3555ccba127f", - "f": "4a0a19218e082a343a1b17e5333409af9d98f0f5", - } + for x in "def": # Make test files with predictable hashes with open(dir3 / x, "w", encoding="ascii") as f: @@ -847,14 +853,7 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: dir4 = tmp_path / "dir_no_info" dir4.mkdir() - sha1 = { - # Expected hashes of ASCII letters (no linefeed) - # as returned from: - # for x in g h i ; do echo -n $x | sha1sum ; done - "g": "54fd1711209fb1c0781092374132c66e79e2241b", - "h": "27d5482eebd075de44389774fce28c69f45c8a75", - "i": "042dc4512fa3d391c5170cf3aa61e6a638f84342", - } + for x in "ghi": # Make test files with predictable hashes with open(dir4 / x, "w", encoding="ascii") as f: @@ -874,9 +873,6 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: # Visualize the path structure list_files(tmp_path) - # check invert? as there should be no data in there - # check_provenance(folder, directory=True) - # Output should include ls stdout of filenames a b c on each line file_list = ( folder @@ -887,8 +883,8 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: # echo -e "a\nb\nc" | sha1sum # 3ca69e8d6c234a469d16ac28a4a658c92267c423 - ) - # File should not exist... - assert not file_list.is_file() + + assert file_list.is_file() # Input files should be captured by hash value, # even if they were inside a class: Directory @@ -898,8 +894,11 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: # File should be empty and in the future not existing... # assert os.path.getsize(p.absolute()) == 0 # To be discared when file really does not exist anymore - if l not in ['d', 'e', 'f', 'g', 'h', 'i']: - print("Analysing file %s", l) + if l in ['d', 'e', 'f', 'g', 'h', 'i']: + print(f"Analysing file {l}") + assert not p.is_file(), f"Could find {l} as {p}" + else: + print(f"Analysing file {l}") assert p.is_file(), f"Could not find {l} as {p}" def cwltool_no_data(tmp_path: Path, *args: Any) -> Path: diff --git a/tests/test_provenance.py::test_directory_workflow_no_listing b/tests/test_provenance.py::test_directory_workflow_no_listing deleted file mode 100644 index 06df4048d..000000000 --- a/tests/test_provenance.py::test_directory_workflow_no_listing +++ /dev/null @@ -1,32987 +0,0 @@ -versions pytest-7.3.1, python-3.10.11.final.0 -cwd=/Users/jasperk/gitlab/cwltool -args=('--debug', 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nodeid: - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : PytestCollectionWarning("cannot collect test class 'TestFsAccess' because it has a __init__ constructor (from: tests/test_path_checks.py)"), category : 'PytestCollectionWarning', filename : '/Users/jasperk/gitlab/cwltool/tests/test_path_checks.py', lineno : 110, line : None} - when: collect - nodeid: - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_anon_types.py::test_anon_types[snippet0] - location: ('tests/test_anon_types.py', 116, 'test_anon_types[snippet0]') - early skip of rewriting module: _jb_parallel_tree_manager [assertion] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_cuda.py::test_cuda_eval_resource_max', 'location': ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max'), 'keywords': 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'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005695310001101461, 'start': 1685951407.1618838, 'stop': 1685951407.162456, '$report_type': 'TestReport', 'item_index': 81, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo ["bar"])-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo ["bar"])-False]'), 'keywords': {'test_expression_match[(foo ["bar"])-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo ["bar"])-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007806869998603361, 'start': 1685951407.164284, 'stop': 1685951407.165066, '$report_type': 'TestReport', 'item_index': 62, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz'])-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz'])-zab1]"), 'keywords': {"test_expression_interpolate[$(foo.bar['baz'])-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['baz'])-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004662589999497868, 'start': 1685951407.1631842, 'stop': 1685951407.163651, '$report_type': 'TestReport', 'item_index': 81, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish 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'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004903330000161077, 'start': 1685951407.1636748, 'stop': 1685951407.164167, '$report_type': 'TestReport', 'item_index': 101, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_cuda.py::test_cuda_eval_resource_max - location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]"), 'keywords': {"test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].baz)-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006115910000517033, 'start': 1685951407.164877, 'stop': 1685951407.16549, '$report_type': 'TestReport', 'item_index': 82, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]"), 'keywords': {"test_expression_interpolate[$(foo['b\\\\'ar'].baz)-True]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].baz)-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003998640004283516, 'start': 1685951407.166046, 'stop': 1685951407.166448, '$report_type': 'TestReport', 'item_index': 82, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo ["bar"])-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo ["bar"])-False]'), 'keywords': {'test_expression_match[(foo ["bar"])-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo ["bar"])-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003943009996874025, 'start': 1685951407.16566, 'stop': 1685951407.166056, '$report_type': 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'user_properties': [], 'sections': [], 'duration': 0.0006716450006933883, 'start': 1685951407.168631, 'stop': 1685951407.1693041, '$report_type': 'TestReport', 'item_index': 63, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": "zab1"} {"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": 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'tests/test_examples.py::test_expression_interpolate[$(foo["b\'ar"].baz)-True]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\'ar"].baz)-True]'), 'keywords': {'test_expression_interpolate[$(foo["b\'ar"].baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\'ar"].baz)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006500110002889414, 'start': 1685951407.168532, 'stop': 1685951407.169183, '$report_type': 'TestReport', 'item_index': 83, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[( foo["bar"])-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[( 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"tests/test_examples.py::test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]", 'tests/test_examples.py::test_expression_interpolate[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]', 'tests/test_examples.py::test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]', 'tests/test_examples.py::test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]', 'tests/test_examples.py::test_parameter_to_expression[-$(foo.bar)--{"baz":"zab1"}]', 'tests/test_examples.py::test_parameter_ finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["b\'ar"].baz)-True]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\'ar"].baz)-True]'), 'keywords': {'test_expression_interpolate[$(foo["b\'ar"].baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\'ar"].baz)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00042951199975505006, 'start': 1685951407.169718, 'stop': 1685951407.170149, '$report_type': 'TestReport', 'item_index': 83, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo["b\'ar"].baz)-True]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\'ar"].baz)-True]'), 'keywords': {'test_expression_interpolate[$(foo["b\'ar"].baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["b\'ar"].baz)-True': 1, 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1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006886129995109513, 'start': 1685951407.169198, 'stop': 1685951407.169888, '$report_type': 'TestReport', 'item_index': 103, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]'), 'keywords': {'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005928349992245785, 'start': 1685951407.1704981, 'stop': 1685951407.171092, '$report_type': 'TestReport', 'item_index': 103, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]'), 'keywords': {'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz)-None': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008802599995760829, 'start': 1685951407.172412, 'stop': 1685951407.173294, '$report_type': 'TestReport', 'item_index': 84, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] -ÐV@V°V V V!VPúTp!V°úTûTpûTÐûT0üTà!V0qF°èU0éU°éU0êUP"VüTÀ"V0#VðüTPýT #V°ýTþT$VpþTÐþT€$V0ÿTð$V`%VÐ%V@&VÿT°êU0ëU0@V°&V 'V'V(Vp(Và(V pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]'), 'keywords': {'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003808780002145795, 'start': 1685951407.1716611, 'stop': 1685951407.172043, '$report_type': 'TestReport', 'item_index': 103, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo[bar].baz)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo[bar].baz)-False]'), 'keywords': {'test_expression_match[(foo[bar].baz)-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo[bar].baz)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009385580005982774, 'start': 1685951407.1726239, 'stop': 1685951407.173565, '$report_type': 'TestReport', 'item_index': 64, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo[bar].baz)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo[bar].baz)-False]'), 'keywords': {'test_expression_match[(foo[bar].baz)-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo[bar].baz)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000691512000230432, 'start': 1685951407.174499, 'stop': 1685951407.175193, '$report_type': 'TestReport', 'item_index': 64, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]'), 'keywords': {'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz)-None': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003795280008489499, 'start': 1685951407.175756, 'stop': 1685951407.176137, '$report_type': 'TestReport', 'item_index': 84, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo['b\\'ar'].baz)--true] - location: ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['b\\\\'ar'].baz)--true]") - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo[bar].baz)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo[bar].baz)-False]'), 'keywords': {'test_expression_match[(foo[bar].baz)-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo[bar].baz)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00034629699985089246, 'start': 1685951407.1757581, 'stop': 1685951407.176105, '$report_type': 'TestReport', 'item_index': 64, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] -ession_interpolate[-$(foo['b\\\\'ar'].baz)--true]", 'tests/test_examples.py::test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]', 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]', 'tests/test_examples.py::test_expression_interpolate[$(foo.bar) $(foo.bar)-{"baz": "zab1"} {"baz": "zab1"}]', 'tests/test_examples.py::test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]', 'tests/test_examples.py::test_expression_interpolate[$(foo["bar"]) $(foo["bar"])-{"baz": 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'user_properties': [], 'sections': [], 'duration': 0.00036646900025516516, 'start': 1685951407.185961, 'stop': 1685951407.1863291, '$report_type': 'TestReport', 'item_index': 67, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(lst['length'])-2]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(lst['length'])-2]"), 'keywords': {"test_expression_interpolate[$(lst['length'])-2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(lst['length'])-2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00032855400058906525, 'start': 1685951407.189135, 'stop': 1685951407.189465, '$report_type': 'TestReport', 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object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.bar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.bar)-False]'), 'keywords': {'test_expression_match[foo.bar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008627580000393209, 'start': 1685951407.1903841, 'stop': 1685951407.191249, '$report_type': 'TestReport', 'item_index': 69, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.bar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.bar)-False]'), 'keywords': {'test_expression_match[foo.bar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004924349996144883, 'start': 1685951407.192138, 'stop': 1685951407.192632, '$report_type': 'TestReport', 'item_index': 69, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.bar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.bar)-False]'), 'keywords': {'test_expression_match[foo.bar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.bar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003537920001690509, 'start': 1685951407.1931489, 'stop': 1685951407.193504, '$report_type': 'TestReport', 'item_index': 69, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.b ar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.b ar)-False]'), 'keywords': {'test_expression_match[foo.b ar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.b ar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005005540006095544, 'start': 1685951407.194539, 'stop': 1685951407.195041, '$report_type': 'TestReport', 'item_index': 70, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.b ar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.b ar)-False]'), 'keywords': {'test_expression_match[foo.b ar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.b ar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003098170000157552, 'start': 1685951407.195513, 'stop': 1685951407.1958241, '$report_type': 'TestReport', 'item_index': 70, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz'])-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz'])-zab1]"), 'keywords': {"test_expression_interpolate[$(foo.bar['baz'])-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['baz'])-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005695310001101461, 'start': 1685951407.1618838, 'stop': 1685951407.162456, '$report_type': 'TestReport', 'item_index': 81, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo ["bar"])-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo 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'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004662589999497868, 'start': 1685951407.1631842, 'stop': 1685951407.163651, '$report_type': 'TestReport', 'item_index': 81, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] -Õرnify Úر1th)HÕرondit Úر1PrechÕرshead Úر1)iˆÕر EntpÞUezEntity is - -equeÚongzÚ -uppoÈÕرpNTity - -jform0equekot S0CannXÖرleque0zxÖرm Fai0cond˜Öرnnot 0)i¢¸Öرoeapo0fuseØÖرsffee0is aø pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar']) $(foo['bar'])-{"baz": "zab1"} {"baz": "zab1"}] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz": "zab1"} {"baz": "zab1"}]') - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[foo.b ar)-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[foo.b ar)-False]'), 'keywords': {'test_expression_match[foo.b ar)-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.b ar)-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003831390004052082, 'start': 1685951407.196325, 'stop': 1685951407.1967092, '$report_type': 'TestReport', 'item_index': 70, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar)--{"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007611769997311058, 'start': 1685951407.192053, 'stop': 1685951407.192816, '$report_type': 'TestReport', 'item_index': 89, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo.bar)--{"baz": 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"zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\'])--{"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00033905500004038913, 'start': 1685951407.197654, 'stop': 1685951407.197995, '$report_type': 'TestReport', 'item_index': 90, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]", 'location': ('tests/test_examples.py', 121, 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[hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_match[foo.b'ar)-False]", 'location': ('tests/test_examples.py', 64, "test_expression_match[foo.b'ar)-False]"), 'keywords': {"test_expression_match[foo.b'ar)-False]": 1, 'parametrize': 1, 'pytestmark': 1, "foo.b'ar)-False": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00035343100080353906, 'start': 1685951407.1993961, 'stop': 1685951407.199751, '$report_type': 'TestReport', 'item_index': 71, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]', 'location': 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<_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]'), 'keywords': {'test_expression_interpolate[-$(foo["bar"])--{"baz": "zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["bar"])--{"baz": "zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00033932099995581666, 'start': 1685951407.200981, 'stop': 1685951407.201321, '$report_type': 'TestReport', 'item_index': 91, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo+bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo+bar-False]'), 'keywords': {'test_expression_match[(foo+bar-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo+bar-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003839760001937975, 'start': 1685951407.200552, 'stop': 1685951407.200937, '$report_type': 'TestReport', 'item_index': 72, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo+bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo+bar-False]'), 'keywords': {'test_expression_match[(foo+bar-False]': 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None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005919989998801611, 'start': 1685951407.202494, 'stop': 1685951407.203087, '$report_type': 'TestReport', 'item_index': 92, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_match[(foo+bar-False]', 'location': ('tests/test_examples.py', 64, 'test_expression_match[(foo+bar-False]'), 'keywords': {'test_expression_match[(foo+bar-False]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo+bar-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00041151400000671856, 'start': 1685951407.2019148, 'stop': 1685951407.202328, '$report_type': 'TestReport', 'item_index': 72, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz'])-zab1] - location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz'])-zab1]") - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo.bar.baz)--zab1]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar.baz)--zab1]'), 'keywords': {'test_expression_interpolate[-$(foo.bar.baz)--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.baz)--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 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tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\"ar'].baz)-None] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz)-None]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[( foo["bar"])-False] - location: ('tests/test_examples.py', 64, 'test_expression_match[( foo["bar"])-False]') - finish 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- report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]'), 'keywords': {'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].baz)--null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001641023999582103, 'start': 1685951407.2567759, 'stop': 1685951407.258422, '$report_type': 'TestReport', 'item_index': 99, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(lst[1])-B] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst[1])-B]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz)-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz)-zab1]"), 'keywords': {"test_expression_interpolate[$(foo['bar'].baz)-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz)-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011922129997401498, 'start': 1685951407.258692, 'stop': 1685951407.2599082, '$report_type': 'TestReport', 'item_index': 79, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]'), 'keywords': {'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].baz)--null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000932054000259086, 'start': 1685951407.2593322, 'stop': 1685951407.260267, '$report_type': 'TestReport', 'item_index': 99, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(lst.length)-2] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst.length)-2]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz)-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz)-zab1]"), 'keywords': {"test_expression_interpolate[$(foo['bar'].baz)-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz)-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005645649998768931, 'start': 1685951407.260633, 'stop': 1685951407.2612, '$report_type': 'TestReport', 'item_index': 79, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]', 'location': ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]'), 'keywords': {'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].baz)--null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00041843700000754325, 'start': 1685951407.260957, 'stop': 1685951407.261378, '$report_type': 'TestReport', 'item_index': 99, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar']["baz"]) $(foo['bar']["baz"])-zab1 zab1] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'bar\']["baz"]) $(foo[\'bar\']["baz"])-zab1 zab1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz)-zab1]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz)-zab1]"), 'keywords': {"test_expression_interpolate[$(foo['bar'].baz)-zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['bar'].baz)-zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005214060001890175, 'start': 1685951407.261953, 'stop': 1685951407.2624772, '$report_type': 'TestReport', 'item_index': 79, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]'), 'keywords': {'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']["bazz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004066560004503117, 'start': 1685951407.2626, 'stop': 1685951407.263008, '$report_type': 'TestReport', 'item_index': 160, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]'), 'keywords': {'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']["bazz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005061390002083499, 'start': 1685951407.264887, 'stop': 1685951407.265397, '$report_type': 'TestReport', 'item_index': 160, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b\\\\'ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006696979999105679, 'start': 1685951407.2652879, 'stop': 1685951407.265959, '$report_type': 'TestReport', 'item_index': 177, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b\\\\'ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005427820005934336, 'start': 1685951407.2666292, 'stop': 1685951407.267174, '$report_type': 'TestReport', 'item_index': 177, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]"), 'keywords': {"test_expression_interpolate_failures[$(foo.bar['bazz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['bazz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005516640003406792, 'start': 1685951407.2671092, 'stop': 1685951407.267663, '$report_type': 'TestReport', 'item_index': 161, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] -\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\\\\\x-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]', 'tests/test_examples.py::test_expression_interpolate_failures[$(fooz)]', 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.barz)]', "tests/test_examples.py::test_expression_interpolate_failures[$(foo['barz'])]", 'tests/test_examples.py::test_expression_interpolate_failures[$(foo["barz"])]', 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar.bazz)]', "tests/test_examples.py::test_expression_interpolate_failures[$(foo['bar'].bazz)]", 'tests/test_examples.py::test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]', "tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])]", "tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]", 'tests/test_examples.py::test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]', 'tests/test_examples.py::test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]', 'tests/test_examples.py::test_e pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006098329995438689, 'start': 1685951407.268758, 'stop': 1685951407.26937, '$report_type': 'TestReport', 'item_index': 178, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]"), 'keywords': {"test_expression_interpolate_failures[$(foo.bar['bazz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['bazz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006548279998241924, 'start': 1685951407.2683752, 'stop': 1685951407.269032, '$report_type': 'TestReport', 'item_index': 161, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]"), 'keywords': {"test_expression_interpolate_failures[$(foo.bar['bazz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo.bar['bazz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00042578600005072076, 'start': 1685951407.269708, 'stop': 1685951407.270136, '$report_type': 'TestReport', 'item_index': 161, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005757959997936268, 'start': 1685951407.269971, 'stop': 1685951407.270549, '$report_type': 'TestReport', 'item_index': 178, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004131420000703656, 'start': 1685951407.2712471, 'stop': 1685951407.271662, '$report_type': 'TestReport', 'item_index': 178, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005706130004909937, 'start': 1685951407.2716181, 'stop': 1685951407.272191, '$report_type': 'TestReport', 'item_index': 162, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar].baz)-False] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar].baz)-False]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0009290719999626162, 'start': 1685951407.272831, 'stop': 1685951407.2737632, '$report_type': 'TestReport', 'item_index': 162, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(lst.length)-2] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(lst.length)-2]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007420629999614903, 'start': 1685951407.273581, 'stop': 1685951407.274325, '$report_type': 'TestReport', 'item_index': 179, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b\\\\'ar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006088889995226054, 'start': 1685951407.27457, 'stop': 1685951407.275181, '$report_type': 'TestReport', 'item_index': 162, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1] - location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo.bar['baz']) $(foo.bar['baz'])-zab1 zab1]") - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]': 1, 'parametrize': 1, 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[], 'duration': 0.000394663000406581, 'start': 1685951407.2837, 'stop': 1685951407.284096, '$report_type': 'TestReport', 'item_index': 164, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008642109996799263, 'start': 1685951407.283328, 'stop': 1685951407.284194, '$report_type': 'TestReport', 'item_index': 181, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006055339999875287, 'start': 1685951407.2848902, 'stop': 1685951407.2854981, '$report_type': 'TestReport', 'item_index': 181, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(lst[O])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[O])]'), 'keywords': {'test_expression_interpolate_failures[$(lst[O])]': 1, 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'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008366640004169312, 'start': 1685951407.29308, 'stop': 1685951407.293918, '$report_type': 'TestReport', 'item_index': 183, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(lst['length'])-2] - location: 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pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000552768000488868, 'start': 1685951407.296146, 'stop': 1685951407.296701, '$report_type': 'TestReport', 'item_index': 183, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(lst['lengthz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(lst['lengthz'])]"), 'keywords': {"test_expression_interpolate_failures[$(lst['lengthz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(lst['lengthz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005254800007605809, 'start': 1685951407.297803, 'stop': 1685951407.29833, '$report_type': 'TestReport', 'item_index': 168, 'worker_id': 'gw4', 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finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-$foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00045144300020183437, 'start': 1685951407.299617, 'stop': 1685951407.3000698, '$report_type': 'TestReport', 'item_index': 184, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - 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'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo.bar-False] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar-False]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-$foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005127379999976256, 'start': 1685951407.3006878, 'stop': 1685951407.3012018, '$report_type': 'TestReport', 'item_index': 184, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2] - location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]") - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo.barz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.barz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo.barz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.barz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012037999995300197, 'start': 1685951407.3027682, 'stop': 1685951407.303977, '$report_type': 'TestReport', 'item_index': 169, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\foo-foo-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-foo-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\foo-foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012132620004194905, 'start': 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'tests/test_examples.py::test_expression_interpolate_failures[-$(foo["barz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["barz"])]'), 'keywords': {'test_expression_interpolate_failures[-$(foo["barz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["barz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004024009995191591, 'start': 1685951407.316164, 'stop': 1685951407.3165681, '$report_type': 'TestReport', 'item_index': 171, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 278, 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{'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005338979999578441, 'start': 1685951407.317007, 'stop': 1685951407.317543, '$report_type': 'TestReport', 'item_index': 187, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[foo.b ar)-False] - location: ('tests/test_examples.py', 64, 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0.0008858649998728652, 'start': 1685951407.3192792, 'stop': 1685951407.3201668, '$report_type': 'TestReport', 'item_index': 188, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar.bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.bar.bazz)]'), 'keywords': {'test_expression_interpolate_failures[-$(foo.bar.bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000410487000408466, 'start': 1685951407.320811, 'stop': 1685951407.321223, '$report_type': 'TestReport', 'item_index': 172, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00044027899912180146, 'start': 1685951407.32071, 'stop': 1685951407.321152, '$report_type': 'TestReport', 'item_index': 188, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} -rize': 1, 'pytestmark': 1, '$(lst[O])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'lonrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00043068799914181, 'start': 1685951407.2861109, 'stop': 1685951407.2865438, '$report_type': 'TestReport', 'item_index': 165, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} -pV£À3§Höãy`1V°V£4§Äf£ÊÊËp6M`4§i./? ÞðV£ finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004889510000793962, 'start': 1685951407.321783, 'stop': 1685951407.322273, '$report_type': 'TestReport', 'item_index': 188, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['bar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['bar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006149490000098012, 'start': 1685951407.3226628, 'stop': 1685951407.3232799, '$report_type': 'TestReport', 'item_index': 173, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['bar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['bar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005227310002737795, 'start': 1685951407.3238761, 'stop': 1685951407.324401, '$report_type': 'TestReport', 'item_index': 173, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008435240006292588, 'start': 1685951407.323806, 'stop': 1685951407.324651, '$report_type': 'TestReport', 'item_index': 189, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar'].bazz)]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['bar'].bazz)]"), 'keywords': {"test_expression_interpolate_failures[-$(foo['bar'].bazz)]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].bazz)": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005881890001546708, 'start': 1685951407.325191, 'stop': 1685951407.325781, '$report_type': 'TestReport', 'item_index': 173, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000570602999687253, 'start': 1685951407.325197, 'stop': 1685951407.32577, '$report_type': 'TestReport', 'item_index': 189, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004434630000105244, 'start': 1685951407.326494, 'stop': 1685951407.3269398, '$report_type': 'TestReport', 'item_index': 189, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2] - location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]'), 'keywords': {'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["bazz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000519357000484888, 'start': 1685951407.327293, 'stop': 1685951407.3278148, '$report_type': 'TestReport', 'item_index': 174, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar)--{"baz": "zab1"}]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000679273999594443, 'start': 1685951407.32805, 'stop': 1685951407.3287308, '$report_type': 'TestReport', 'item_index': 190, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003356179995535058, 'start': 1685951407.329217, 'stop': 1685951407.3295538, '$report_type': 'TestReport', 'item_index': 190, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]'), 'keywords': {'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["bazz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00038859100004629, 'start': 1685951407.32945, 'stop': 1685951407.3298402, '$report_type': 'TestReport', 'item_index': 174, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004107869999643299, 'start': 1685951407.3301141, 'stop': 1685951407.3305259, '$report_type': 'TestReport', 'item_index': 190, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['bar'])--{"baz": "zab1"}] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\'])--{"baz": "zab1"}]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar['bazz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo.bar['bazz'])]"), 'keywords': {"test_expression_interpolate_failures[-$(foo.bar['bazz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['bazz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008235509994847234, 'start': 1685951407.331155, 'stop': 1685951407.33198, '$report_type': 'TestReport', 'item_index': 175, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_match[foo.b'ar)-False] - location: ('tests/test_examples.py', 64, "test_expression_match[foo.b'ar)-False]") - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009039380001922837, 'start': 1685951407.3321338, 'stop': 1685951407.3330402, '$report_type': 'TestReport', 'item_index': 191, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar['bazz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo.bar['bazz'])]"), 'keywords': {"test_expression_interpolate_failures[-$(foo.bar['bazz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['bazz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006024900003467337, 'start': 1685951407.332716, 'stop': 1685951407.3333209, '$report_type': 'TestReport', 'item_index': 175, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\'ar'].baz) $(foo['b\\'ar'].baz)-true true] - location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['b\\\\'ar'].baz) $(foo['b\\\\'ar'].baz)-true true]") - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005204970002523623, 'start': 1685951407.333714, 'stop': 1685951407.334236, '$report_type': 'TestReport', 'item_index': 191, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo["b\\'ar"].baz) $(foo["b\\'ar"].baz)-true true] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\"ar'].baz) $(foo['b\\"ar'].baz)-null null] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo.bar.baz)--zab1] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo.bar.baz)--zab1]') - finish pytest_runtest_logfinish --> [] [hook] - 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pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['bar'].baz)--zab1] - location: ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['bar'].baz)--zab1]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['bar']["baz"])--zab1] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['b\\"ar'].baz) $(foo['b\\"ar'].baz)-null null] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['bar']["baz"])--zab1] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo bar-False] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo bar-False]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo)-expected0] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo)-expected0]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b'ar":{"baz":true},"b\\"ar":{"baz":null}}] - location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo)--{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b\'ar":{"baz":true},"b\\\\"ar":{"baz":null}}]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo)-expected0] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo)-expected0]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo.bar['baz'])--zab1] - location: ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo.bar['baz'])--zab1]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar)-expected1] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar)-expected1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo.bar['baz'])--zab1] - location: ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo.bar['baz'])--zab1]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - 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finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo["bar"])-expected3] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo["bar"])-expected3]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz)-zab1] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz)-zab1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo.bar.baz)-zab1] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo.bar.baz)-zab1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['b\\"ar'].baz)--null] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz)-zab1] - location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz)-zab1]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[-$(foo['b\\"ar'].baz)--null] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baz)--null]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo['bar'].baz)-zab1] - location: ('tests/test_examples.py', 121, "test_expression_interpolate[$(foo['bar'].baz)-zab1]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['bar']["bazz"])] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\'ar'].bazz)] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\'ar'].bazz)] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['bar']["bazz"])] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\'ar"].bazz)] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\'ar'].bazz)] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\'ar"].bazz)] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\"ar'].bazz)] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'b\\\\"ar\'].bazz)]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\'ar'].bazz)] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['b\\\\'ar'].bazz)]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo["b'ar"].bazz)] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo["b\'ar"].bazz)]') - finish pytest_runtest_logstart --> [] [hook] - 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finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$(foo.bar.baz)-$(foo.bar.baz)-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\x-x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\x-x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.21595973200055596, 'start': 1685951407.1566231, 'stop': 1685951407.372582, '$report_type': 'TestReport', 'item_index': 140, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007626679998793406, 'start': 1685951407.3771882, 'stop': 1685951407.377953, '$report_type': 'TestReport', 'item_index': 141, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['b\\"ar'].bazz)] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'b\\\\"ar\'].bazz)]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-\\zab1-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]'), 'keywords': {'test_parameter_to_expression[-$(foo["b\\\\\'ar"].baz)--true]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["b\\\\\'ar"].baz)--true': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0029614650002258713, 'start': 1685951407.378196, 'stop': 1685951407.3811588, '$report_type': 'TestReport', 'item_index': 121, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst[O])] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[O])]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-\\zab1-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst[O])] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[O])]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'b\\\\"ar\'].baz)--null]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'b\\\\"ar\'].baz)--null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002541908999774023, 'start': 1685951407.3843572, 'stop': 1685951407.386901, '$report_type': 'TestReport', 'item_index': 122, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst[2])] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[2])]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005822630000693607, 'start': 1685951407.3891551, 'stop': 1685951407.389739, '$report_type': 'TestReport', 'item_index': 123, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type1-sink_type1-None-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type1-sink_type1-None-None-warning]'), 'keywords': {'test_typechecking[src_type1-sink_type1-None-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type1-sink_type1-None-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001482418999330548, 'start': 1685951407.3904798, 'stop': 1685951407.391967, '$report_type': 'TestReport', 'item_index': 224, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} -sts/test_examples.py::test_parameter_to_expression_inter`¬\\\\\\\\\\\\\\x-\\\\\\\\x-1]', 'tests/test_examples.py::°[usion_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo÷Kst_examples.py::test_parameter_to_expression_interpolate¬$(foo.bar.baz)-\\\\zab1-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]', 'testÚamples.Úparameter_to_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\\\x-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]', 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[ finish pytest_report_from_serializable --> [hook] - 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finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar) $(foo.bar)-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.003042719000404759, 'start': 1685951407.3904269, 'stop': 1685951407.393472, '$report_type': 'TestReport', 'item_index': 123, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst[2])] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst[2])]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006835909998699208, 'start': 1685951407.395856, 'stop': 1685951407.3965409, '$report_type': 'TestReport', 'item_index': 124, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(lst.lengthz)] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(lst.lengthz)]') -s/test_examples.py::test_expression_interpolate[-$(foo['bar']["baz"])--zab1] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[-$(foo[\'bar\']["baz"])--zab1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo bar-False] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo bar-False]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate[$(foo)-expected0] - location: ('tests/test_examples.py', 121, 'test_expression_interpolate[$(foo)-expected0]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: -$(foo['b\\\\'ar'].baz)--true]", 'tests/test_examples.py::test_expression_interpolate[-$(foo["b\\\\\'ar"].baz)--true]', 'tests/test_examples.py::test_expression_interpolate[-$(foo[\'b\\\\"ar\'].baÚ', 't finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\$(foo.bar.baz)-\\$(foo.bar.baz)-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0022234130001379526, 'start': 1685951407.3977652, 'stop': 1685951407.399989, '$report_type': 'TestReport', 'item_index': 144, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003133230002276832, 'start': 1685951407.400414, 'stop': 1685951407.4007292, '$report_type': 'TestReport', 'item_index': 144, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'bar\']) $(foo[\'bar\'])-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00038902599953871686, 'start': 1685951407.400353, 'stop': 1685951407.400743, '$report_type': 'TestReport', 'item_index': 124, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type3-sink_type3-None-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type3-sink_type3-None-None-pass]'), 'keywords': {'test_typechecking[src_type3-sink_type3-None-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type3-sink_type3-None-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003926070003217319, 'start': 1685951407.40034, 'stop': 1685951407.400734, '$report_type': 'TestReport', 'item_index': 226, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type3-sink_type3-None-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type3-sink_type3-None-None-pass]'), 'keywords': {'test_typechecking[src_type3-sink_type3-None-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type3-sink_type3-None-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005393129995354684, 'start': 1685951407.4012449, 'stop': 1685951407.401786, '$report_type': 'TestReport', 'item_index': 226, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["bar"]) $(foo["bar"])-{"baz":"zab1"} {"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005235139997239457, 'start': 1685951407.4018528, 'stop': 1685951407.402378, '$report_type': 'TestReport', 'item_index': 125, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005191010004637064, 'start': 1685951407.401671, 'stop': 1685951407.4021912, '$report_type': 'TestReport', 'item_index': 145, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type4-sink_type4-None-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type4-sink_type4-None-None-warning]'), 'keywords': {'test_typechecking[src_type4-sink_type4-None-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type4-sink_type4-None-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009563419998812606, 'start': 1685951407.40286, 'stop': 1685951407.403818, '$report_type': 'TestReport', 'item_index': 227, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type4-sink_type4-None-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type4-sink_type4-None-None-warning]'), 'keywords': {'test_typechecking[src_type4-sink_type4-None-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type4-sink_type4-None-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004525889999058563, 'start': 1685951407.404313, 'stop': 1685951407.404767, '$report_type': 'TestReport', 'item_index': 227, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0021481710000443854, 'start': 1685951407.402588, 'stop': 1685951407.404737, '$report_type': 'TestReport', 'item_index': 145, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - 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data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006266170003073057, 'start': 1685951407.413418, 'stop': 1685951407.414047, '$report_type': 'TestReport', 'item_index': 146, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]'), 'keywords': {'test_parameter_to_expression[$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.baz) $(foo.bar.baz)-zab1 zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004931049998049275, 'start': 1685951407.414334, 'stop': 1685951407.414829, '$report_type': 'TestReport', 'item_index': 126, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["bar"])--{"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.004445026000212238, 'start': 1685951407.43843, 'stop': 1685951407.442878, '$report_type': 'TestReport', 'item_index': 114, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_dedupe', 'location': ('tests/test_examples.py', 576, 'test_dedupe'), 'keywords': {'test_dedupe': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0009223950000887271, 'start': 1685951407.44148, 'stop': 1685951407.4424078, '$report_type': 'TestReport', 'item_index': 211, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$foo-$foo-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]'), 'keywords': {'test_parameter_to_expression[-$(foo["bar"])--{"baz":"zab1"}]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo["bar"])--{"baz":"zab1"}': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004895369993391796, 'start': 1685951407.4440808, 'stop': 1685951407.444572, '$report_type': 'TestReport', 'item_index': 114, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]"), 'keywords': {"test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009072579996427521, 'start': 1685951407.44374, 'stop': 1685951407.444653, '$report_type': 'TestReport', 'item_index': 130, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_compare_types[0-source0-sink0-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[0-source0-sink0-True]'), 'keywords': {'test_compare_types[0-source0-sink0-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0-source0-sink0-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011165440000695526, 'start': 1685951407.444523, 'stop': 1685951407.445641, '$report_type': 'TestReport', 'item_index': 212, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['b\\'ar'].bazz)] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['b\\\\'ar'].bazz)]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo['bar']["bazz"])] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo[\'bar\']["bazz"])]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo["b\\'ar"].bazz)] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["b\\\\\'ar"].bazz)]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar['bazz'])] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo.bar['bazz'])]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] -Höãy`1V°V£4§Äf£ÊÊËp6M`4§i finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo.bar.baz)--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar.baz)--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo.bar.baz)--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.baz)--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000905028000488528, 'start': 1685951407.446458, 'stop': 1685951407.447365, '$report_type': 'TestReport', 'item_index': 115, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]"), 'keywords': {"test_parameter_to_expression[$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['b ar'].baz) $(foo['b ar'].baz)-2 2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0008037950001380523, 'start': 1685951407.4498649, 'stop': 1685951407.4506721, '$report_type': 'TestReport', 'item_index': 130, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo.bar.baz)--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar.baz)--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo.bar.baz)--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.baz)--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.004031694999866886, 'start': 1685951407.447961, 'stop': 1685951407.451995, '$report_type': 'TestReport', 'item_index': 115, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\foo-foo-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-foo-1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo.bar.baz)--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo.bar.baz)--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo.bar.baz)--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo.bar.baz)--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004981169995517121, 'start': 1685951407.452596, 'stop': 1685951407.453096, '$report_type': 'TestReport', 'item_index': 115, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.barz)]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type12-sink_type12-merge_flattened-None-warning]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type12-sink_type12-merge_flattened-None-warning]'), 'keywords': {'test_typechecking[src_type12-sink_type12-merge_flattened-None-warning]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type12-sink_type12-merge_flattened-None-warning': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014149050002743024, 'start': 1685951407.45079, 'stop': 1685951407.452208, '$report_type': 'TestReport', 'item_index': 235, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["baz"])--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006352569998853141, 'start': 1685951407.470835, 'stop': 1685951407.471473, '$report_type': 'TestReport', 'item_index': 117, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type13-sink_type13-merge_flattened-None-exception]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type13-sink_type13-merge_flattened-None-exception]'), 'keywords': {'test_typechecking[src_type13-sink_type13-merge_flattened-None-exception]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type13-sink_type13-merge_flattened-None-exception': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00045605000013893005, 'start': 1685951407.45876, 'stop': 1685951407.45922, '$report_type': 'TestReport', 'item_index': 236, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(fooz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(fooz)]'), 'keywords': {'test_expression_interpolate_failures[$(fooz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(fooz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006368700005623396, 'start': 1685951407.474289, 'stop': 1685951407.4749281, '$report_type': 'TestReport', 'item_index': 154, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(fooz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(fooz)]'), 'keywords': {'test_expression_interpolate_failures[$(fooz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(fooz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0008318189993588021, 'start': 1685951407.475588, 'stop': 1685951407.4764218, '$report_type': 'TestReport', 'item_index': 154, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013473919998432393, 'start': 1685951407.477623, 'stop': 1685951407.4789739, '$report_type': 'TestReport', 'item_index': 134, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0028304689994911314, 'start': 1685951407.479712, 'stop': 1685951407.482545, '$report_type': 'TestReport', 'item_index': 134, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo.bar['baz'])--zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo.bar['baz'])--zab1]"), 'keywords': {"test_parameter_to_expression[-$(foo.bar['baz'])--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['baz'])--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006902869999976247, 'start': 1685951407.473063, 'stop': 1685951407.473755, '$report_type': 'TestReport', 'item_index': 118, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo.bar['baz'])--zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo.bar['baz'])--zab1]"), 'keywords': {"test_parameter_to_expression[-$(foo.bar['baz'])--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo.bar['baz'])--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005814630003442289, 'start': 1685951407.47889, 'stop': 1685951407.4794738, '$report_type': 'TestReport', 'item_index': 118, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$(foo.bar.baz)-$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0011832519994641189, 'start': 1685951407.483479, 'stop': 1685951407.484666, '$report_type': 'TestReport', 'item_index': 134, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\$(foo.bar.baz)-\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000916687999961141, 'start': 1685951407.487365, 'stop': 1685951407.4882839, '$report_type': 'TestReport', 'item_index': 135, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo['b ar'].baz)--2]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['b ar'].baz)--2]"), 'keywords': {"test_parameter_to_expression[-$(foo['b ar'].baz)--2]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b ar'].baz)--2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.004785899000125937, 'start': 1685951407.482217, 'stop': 1685951407.487005, '$report_type': 'TestReport', 'item_index': 119, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.barz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo.barz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo.barz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.barz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005517300005521975, 'start': 1685951407.4811351, 'stop': 1685951407.481688, '$report_type': 'TestReport', 'item_index': 155, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: -erpolate_failures[-$(foo['barz'])]" when='teardown' outcome='passed'> [hook] - [hook] - pytest_report_from_serializable ÚÚ<_pytest.config.Config object at 0x11074ef80> - ¬/test_examples.py::test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]", 'location': ('tests/test_examples.py', 121, "test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]"), 'keywords': {"test_expression_interpolate[-$(foo['b\\\\'ar'].baz)--true]": 1, 'parametrize': 1, 'pyt pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_compare_types[record 1-source5-sink5-False]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[record 1-source5-sink5-False]'), 'keywords': {'test_compare_types[record 1-source5-sink5-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'record 1-source5-sink5-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005380510001486982, 'start': 1685951407.4761322, 'stop': 1685951407.476672, '$report_type': 'TestReport', 'item_index': 217, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_parameter_to_expression[-$(foo['b ar'].baz)--2]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['b ar'].baz)--2]"), 'keywords': {"test_parameter_to_expression[-$(foo['b ar'].baz)--2]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['b ar'].baz)--2": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004766259999087197, 'start': 1685951407.487801, 'stop': 1685951407.48828, '$report_type': 'TestReport', 'item_index': 119, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] -ter_to_expression[-$(foo['bar'].baz)--zab1]", 'location': ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['bar'].baz)--zab1]"), 'keywords': {"test_parameter_to_expression[-$(foo['bar'].baz)--zab1]": 1, 'parametrize': 1, 'pytestmark': 1, "-$(foo['bar'].baz)--zab1": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006598230002055061, 'start': 1685951407.461045, 'stop': 1685951407.461707, '$report_type': 'TestReport', 'item_index': 116, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['barz'])] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['barz'])]") - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_compare_types[2-source2-sink2-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[2-source2-sink2-True]'), 'keywords': {'test_compare_types[2-source2-sink2-True]': 1, 'parametrize': 1, 'pytestmark': 1, '2-source2-sink2-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000625794999905338, 'start': 1685951407.45877, 'stop': 1685951407.459397, '$report_type': 'TestReport', 'item_index': 214, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] -ssed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002835494999999355, 'start': 1685 pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_examples.py::test_expression_interpolate_failures[$(foo['barz'])]", 'location': ('tests/test_examples.py', 248, "test_expression_interpolate_failures[$(foo['barz'])]"), 'keywords': {"test_expression_interpolate_failures[$(foo['barz'])]": 1, 'parametrize': 1, 'pytestmark': 1, "$(foo['barz'])": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013087470006212243, 'start': 1685951407.485544, 'stop': 1685951407.486857, '$report_type': 'TestReport', 'item_index': 156, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011623079999480979, 'start': 1685951407.49646, 'stop': 1685951407.497626, '$report_type': 'TestReport', 'item_index': 136, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002443803999994998, 'start': 1685951407.4981608, 'stop': 1685951407.500606, '$report_type': 'TestReport', 'item_index': 136, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005341539999790257, 'start': 1685951407.501076, 'stop': 1685951407.501611, '$report_type': 'TestReport', 'item_index': 136, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007855650001147296, 'start': 1685951407.489816, 'stop': 1685951407.490603, '$report_type': 'TestReport', 'item_index': 193, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] -74ef80> - data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type10-Any-merge_nested-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type10-Any-merge_nested-None-pass]'), 'keywords': {'test_typechecking[src_type10-Any-merge_nested-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type10-Any-merge_nested-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006485630001407117, 'start': 1685951407.439878, 'stop': 1685951407.4405289, '$report_type': 'TestReport', 'item_index': 233, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$foo-$foo-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-$foo pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[0-source0-sink0-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[0-source0-sink0-True]'), 'keywords': {'test_compare_types_strict[0-source0-sink0-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0-source0-sink0-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012504549995355774, 'start': 1685951407.4789708, 'stop': 1685951407.480224, '$report_type': 'TestReport', 'item_index': 218, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007740010005363729, 'start': 1685951407.492597, 'stop': 1685951407.493373, '$report_type': 'TestReport', 'item_index': 193, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo["barz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo["barz"])]'), 'keywords': {'test_expression_interpolate_failures[$(foo["barz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["barz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005903749997742125, 'start': 1685951407.491008, 'stop': 1685951407.4915998, '$report_type': 'TestReport', 'item_index': 157, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] -ion': 0.0012149430003773887, 'start': 1685951407.462949, 'stop': 1685951407.4641678, '$report_type': 'TestReport', 'item_index': 215, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]'), 'keywords': {'test_parameter_to_expression[-$(foo[\'bar\']["baz"])--zab1]': 1, 'parametrize': 1, 'pytestmark': 1, '-$(foo[\'bar\']["baz"])--zab1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015898760002528434, 'start': 1685951407.46432, 'stop': 1685951407.465913, '$report_type': 'TestReport', 'item_index': 117, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\x-x-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\x-x-1]') - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\x-\\\\\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007493510001950199, 'start': 1685951407.471963, 'stop': 1685951407.472715, '$report_type': 'TestReport', 'item_index': 153, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]', 'location': ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]'), 'keywords': {'test_parameter_to_expression[$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo[\'b\\\\"ar\'].baz) $(foo[\'b\\\\"ar\'].baz)-null null': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005360660006772378, 'start': 1685951407.475329, 'stop': 1685951407.4758668, '$report_type': 'TestReport', 'item_index': 133, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[0-source0-sink0-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[0-source0-sink0-True]'), 'keywords': {'test_compare_types_strict[0-source0-sink0-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0-source0-sink0-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005703129991161404, 'start': 1685951407.480953, 'stop': 1685951407.481526, '$report_type': 'TestReport', 'item_index': 218, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-\\\\$foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003057240000998718, 'start': 1685951407.498126, 'stop': 1685951407.498433, '$report_type': 'TestReport', 'item_index': 194, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo["barz"])]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo["barz"])]'), 'keywords': {'test_expression_interpolate_failures[$(foo["barz"])]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo["barz"])': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00044038600026397035, 'start': 1685951407.4921641, 'stop': 1685951407.492606, '$report_type': 'TestReport', 'item_index': 157, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar.bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo.bar.bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo.bar.bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001430157999493531, 'start': 1685951407.495042, 'stop': 1685951407.496477, '$report_type': 'TestReport', 'item_index': 158, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar.bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo.bar.bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo.bar.bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00046733999988646246, 'start': 1685951407.497409, 'stop': 1685951407.497877, '$report_type': 'TestReport', 'item_index': 158, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\$foo-\\\\$foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-\\\\$foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005012780002289219, 'start': 1685951407.498927, 'stop': 1685951407.49943, '$report_type': 'TestReport', 'item_index': 194, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\x-\\x-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['barz'])] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['barz'])]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[0-source0-sink0-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[0-source0-sink0-True]'), 'keywords': {'test_compare_types_strict[0-source0-sink0-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0-source0-sink0-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005009080005038413, 'start': 1685951407.482143, 'stop': 1685951407.482645, '$report_type': 'TestReport', 'item_index': 218, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\\\\\\\\\$(foo.bar.baz)-\\\\\\\\zab1-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.002640106999933778, 'start': 1685951407.504642, 'stop': 1685951407.507284, '$report_type': 'TestReport', 'item_index': 137, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]', 'location': ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]'), 'keywords': {'test_parameter_to_expression_interpolate_escapebehavior[\\\\$foo-$foo-1]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\$foo-$foo-1': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008419430005233153, 'start': 1685951407.510935, 'stop': 1685951407.511779, '$report_type': 'TestReport', 'item_index': 138, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.bar.bazz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo.bar.bazz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo.bar.bazz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.bar.bazz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004244880001351703, 'start': 1685951407.498385, 'stop': 1685951407.4988108, '$report_type': 'TestReport', 'item_index': 158, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-\\\\foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005957029998171492, 'start': 1685951407.5008461, 'stop': 1685951407.5014431, '$report_type': 'TestReport', 'item_index': 195, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-\\\\foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004010249995189952, 'start': 1685951407.501905, 'stop': 1685951407.5023072, '$report_type': 'TestReport', 'item_index': 195, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\foo-\\\\foo-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\foo-\\\\foo-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005769700001110323, 'start': 1685951407.502945, 'stop': 1685951407.503524, '$report_type': 'TestReport', 'item_index': 195, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[1-source1-sink1-True]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[1-source1-sink1-True]'), 'keywords': {'test_compare_types_strict[1-source1-sink1-True]': 1, 'parametrize': 1, 'pytestmark': 1, '1-source1-sink1-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0021377479997681803, 'start': 1685951407.484278, 'stop': 1685951407.486421, '$report_type': 'TestReport', 'item_index': 219, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] -ord 0-source4-sink4-True]', 'location': ('tests/test_examples.py', 648, 'test_compare_types[record 0-source4-sink4-True]'), 'keywords': {'test_compare_types[record 0-source4-sink4-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'record 0-source4-sink4-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007126489999791374, 'start': 1685951407.470677, 'stop': 1685951407.471393, '$report_type': 'TestReport', 'item_index': 216, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_failures[$(foo.barz)]', 'location': ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[$(foo.barz)]'), 'keywords': {'test_expression_interpolate_failures[$(foo.barz)]': 1, 'parametrize': 1, 'pytestmark': 1, '$(foo.barz)': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006304079997789813, 'start': 1685951407.4798121, 'stop': 1685951407.480444, '$report_type': 'TestReport', 'item_index': 155, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[4-source4-sink4-False]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[4-source4-sink4-False]'), 'keywords': {'test_compare_types_strict[4-source4-sink4-False]': 1, 'parametrize': 1, 'pytestmark': 1, '4-source4-sink4-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004853569998886087, 'start': 1685951407.502296, 'stop': 1685951407.502783, '$report_type': 'TestReport', 'item_index': 222, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_compare_types_strict[4-source4-sink4-False]', 'location': ('tests/test_examples.py', 674, 'test_compare_types_strict[4-source4-sink4-False]'), 'keywords': {'test_compare_types_strict[4-source4-sink4-False]': 1, 'parametrize': 1, 'pytestmark': 1, '4-source4-sink4-False': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007194259997049812, 'start': 1685951407.503436, 'stop': 1685951407.504158, '$report_type': 'TestReport', 'item_index': 222, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009104320006372291, 'start': 1685951407.508001, 'stop': 1685951407.508914, '$report_type': 'TestReport', 'item_index': 197, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - 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data: {'nodeid': 'tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]', 'location': ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]'), 'keywords': {'test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]': 1, 'parametrize': 1, 'pytestmark': 1, '\\\\\\\\x-\\\\x-2': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004891950002274825, 'start': 1685951407.5112882, 'stop': 1685951407.511779, '$report_type': 'TestReport', 'item_index': 197, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo["barz"])] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo["barz"])]') - 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finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar.bazz)] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo.bar.bazz)]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar'].bazz)] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['bar'].bazz)]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - 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finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar'].bazz)] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo['bar'].bazz)]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar']["bazz"])] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-1] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\\\\\x-\\\\\\\\x-1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$(foo.bar.baz)-$(foo.bar.baz)-2] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]') - finish pytest_runtest_logstart --> [] [hook] - 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pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo['bar']["bazz"])] - location: ('tests/test_examples.py', 248, 'test_expression_interpolate_failures[-$(foo[\'bar\']["bazz"])]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\$(foo.bar.baz)-$(foo.bar.baz)-2] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-$(foo.bar.baz)-2]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-\\zab1-2] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar['bazz'])] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo.bar['bazz'])]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\$(foo.bar.baz)-\\zab1-2] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\$(foo.bar.baz)-\\\\zab1-2]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_failures[-$(foo.bar['bazz'])] - location: ('tests/test_examples.py', 248, "test_expression_interpolate_failures[-$(foo.bar['bazz'])]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_interpolate_escapebehavior[\\\\\\$(foo.bar.baz)-\\$(foo.bar.baz)-2] - location: ('tests/test_examples.py', 278, 'test_expression_interpolate_escapebehavior[\\\\\\\\\\\\$(foo.bar.baz)-\\\\$(foo.bar.baz)-2]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_parameter_to_expression[-$(foo['b\\'ar'].baz)--true] - location: ('tests/test_examples.py', 156, "test_parameter_to_expression[-$(foo['b\\\\'ar'].baz)--true]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - 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finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_parameter_to_expression[$(foo["b\\'ar"].baz) $(foo["b\\'ar"].baz)-true true] - location: ('tests/test_examples.py', 156, 'test_parameter_to_expression[$(foo["b\\\\\'ar"].baz) $(foo["b\\\\\'ar"].baz)-true true]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type0-sink_type0-None-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type0-sink_type0-None-None-pass]'), 'keywords': {'test_typechecking[src_type0-sink_type0-None-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type0-sink_type0-None-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000973234999946726, 'start': 1685951407.60507, 'stop': 1685951407.606045, '$report_type': 'TestReport', 'item_index': 223, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_typechecking[src_type0-sink_type0-None-None-pass]', 'location': ('tests/test_examples.py', 803, 'test_typechecking[src_type0-sink_type0-None-None-pass]'), 'keywords': {'test_typechecking[src_type0-sink_type0-None-None-pass]': 1, 'parametrize': 1, 'pytestmark': 1, 'src_type0-sink_type0-None-None-pass': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004977159996997216, 'start': 1685951407.606591, 'stop': 1685951407.60709, '$report_type': 'TestReport', 'item_index': 223, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_parameter_to_expression_interpolate_escapebehavior[\\\\x-\\x-2] - location: ('tests/test_examples.py', 197, 'test_parameter_to_expression_interpolate_escapebehavior[\\\\\\\\x-\\\\x-2]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: [] [hook] - finish pytest_collection_finish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : DeprecationWarning("the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses"), category : 'DeprecationWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/util/path/__init__.py', lineno : 5, line : None} - nodeid: - when: collect - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : PytestCollectionWarning("cannot collect test class 'TestFsAccess' because it has a __init__ constructor (from: tests/test_path_checks.py)"), category : 'PytestCollectionWarning', filename : '/Users/jasperk/gitlab/cwltool/tests/test_path_checks.py', lineno : 110, line : None} - nodeid: - when: collect - location: None - finish pytest_warning_recorded --> [] [hook] - finish pytest_collection --> None [hook] - pytest_runtestloop [hook] - session: testsfailed=0 testscollected=664> - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_cuda.py::test_cuda_eval_resource_max - location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10238f730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10238f730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_cuda.py::test_cuda_eval_resource_max - location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') - keywords: {'test_cuda_eval_resource_max': 1, 'test_cuda.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0007633309996890603 - start: 1685951407.1543272 - stop: 1685951407.155093 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - early skip of rewriting module: rdflib.plugins.stores.memory [assertion] - 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location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') - keywords: {'test_cuda_eval_resource_max': 1, 'test_cuda.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:07]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl'")] - duration: 1.8660347249997358 - start: 1685951407.155669 - stop: 1685951409.021659 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10238f730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10238f730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_cuda.py::test_cuda_eval_resource_max - location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') - keywords: {'test_cuda_eval_resource_max': 1, 'test_cuda.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:07]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nvidia-smi-max.cwl'")] - duration: 0.00017870200008474058 - start: 1685951409.022088 - stop: 1685951409.0222669 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_cuda.py::test_cuda_eval_resource_max - location: ('tests/test_cuda.py', 302, 'test_cuda_eval_resource_max') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_cwl_version.py::test_missing_cwl_version - location: ('tests/test_cwl_version.py', 5, 'test_missing_cwl_version') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10238f730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10238f730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_cwl_version.py::test_missing_cwl_version - location: ('tests/test_cwl_version.py', 5, 'test_missing_cwl_version') - keywords: {'test_missing_cwl_version': 1, 'test_cwl_version.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00023546400007035118 - start: 1685951409.0230908 - stop: 1685951409.023328 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10238f730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10238f730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_cwl_version.py::test_missing_cwl_version - location: ('tests/test_cwl_version.py', 5, 'test_missing_cwl_version') - keywords: {'test_missing_cwl_version': 1, 'test_cwl_version.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/missing_cwlVersion.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing_cwlVersion.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\nNo cwlVersion found. Use the following syntax in your CWL document to declare the version: cwlVersion: .\nNote: if this is a CWL draft-3 (pre v1.0) document then it will need to be upgraded first using https://pypi.org/project/cwl-upgrader/ . 'sbg:draft-2' documents can be upgraded using https://pypi.org/project/sevenbridges-cwl-draft2-upgrader/ .\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/missing_cwlVersion.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing_cwlVersion.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nNo cwlVersion found. Use the following syntax in your CWL document to declare the version: cwlVersion: .\nNote: if this is a CWL draft-3 (pre v1.0) document then it will need to be upgraded first using https://pypi.org/project/cwl-upgrader/ . 'sbg:draft-2' documents can be upgraded using https://pypi.org/project/sevenbridges-cwl-draft2-upgrader/ .")] - duration: 0.021530796000661212 - start: 1685951409.0237088 - stop: 1685951409.0452402 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10238f730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10238f730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_cwl_version.py::test_missing_cwl_version - location: ('tests/test_cwl_version.py', 5, 'test_missing_cwl_version') - keywords: {'test_missing_cwl_version': 1, 'test_cwl_version.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_propert pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_anon_types.py::test_anon_types[snippet1] - location: ('tests/test_anon_types.py', 116, 'test_anon_types[snippet1]') - keywords: {'test_anon_types[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_anon_types.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00022551999973075 - start: 1685951408.172648 - stop: 1685951408.172874 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_anon_types.py::test_anon_types[snippet1] - location: ('tests/test_anon_types.py', 116, 'test_anon_types[snippet1]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_check.py::test_output_checking[tests/wf/badout1.cwl] - location: ('tests/test_check.py', 10, 'test_output_checking[tests/wf/badout1.cwl]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> tests/wf/badout1.cwl [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_check.py::test_output_checking[tests/wf/badout1.cwl] - location: ('tests/test_check.py', 10, 'test_output_checking[tests/wf/badout1.cwl]') - keywords: {'test_output_checking[tests/wf/badout1.cwl]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/badout1.cwl': 1, 'test_check.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00032512599955225596 - start: 1685951408.1741178 - stop: 1685951408.174444 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_check.py::test_output_checking[tests/wf/badout1.cwl] - location: ('tests/test_check.py', 10, 'test_output_checking[tests/wf/badout1.cwl]') - keywords: {'test_output_checking[tests/wf/badout1.cwl]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/badout1.cwl': 1, 'test_check.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/badout1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/badout1.cwl\'\n\x1b[1;30mINFO\x1b[0m [job badout1.cwl] /private/tmp/docker_tmpu35m6j1z$ touch \\\n file1\n\x1b[1;30mERROR\x1b[0m \x1b[31m[job badout1.cwl] Job error:\nError validating output record. Does not exist or is not a File: \'file:///private/tmp/docker_tmpu35m6j1z/file2\'\n in {\n "out": {\n "class": "File",\n "basename": "file2",\n "location": "file:///private/tmp/docker_tmpu35m6j1z/file2",\n "nameroot": "file2",\n "nameext": ""\n }\n}\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job badout1.cwl] completed permanentFail\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/badout1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/badout1.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10238f730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10238f730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_cwl_version.py::test_incorrect_cwl_version - location: ('tests/test_cwl_version.py', 10, 'test_incorrect_cwl_version') - keywords: {'test_incorrect_cwl_version': 1, 'test_cwl_version.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/wrong_cwlVersion.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/wrong_cwlVersion.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\nThe CWL reference runner no longer supports pre CWL v1.0 documents. Supported versions are: \nv1.0\nv1.1\nv1.1.0-dev1 (with --enable-dev flag only)\nv1.2\nv1.2.0-dev1 (with --enable-dev flag only)\nv1.2.0-dev2 (with --enable-dev flag only)\nv1.2.0-dev3 (with --enable-dev flag only)\nv1.2.0-dev4 (with --enable-dev flag only)\nv1.2.0-dev5 (with --enable-dev flag only)\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/wrong_cwlVersion.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/wrong_cwlVersion.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nThe CWL reference runner no longer supports pre CWL v1.0 documents. Supported versions are: \nv1.0\nv1.1\nv1.1.0-dev1 (with --enable-dev flag only)\nv1.2\nv1.2.0-dev1 (with --enable-dev flag only)\nv1.2.0-dev2 (with --enable-dev flag only)\nv1.2.0-dev3 (with --enable-dev flag only)\nv1.2.0-dev4 (with --enable-dev flag only)\nv1.2.0-dev5 (with --enable-dev flag only)")] - duration: 0.0001786439997886191 - start: 1685951409.067976 - stop: 1685951409.0681548 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_cwl_version.py::test_incorrect_cwl_version - location: ('tests/test_cwl_version.py', 10, 'test_incorrect_cwl_version') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_basic[crt_params0] - location: ('tests/test_environment.py', 191, 'test_basic[crt_params0]') - keywords: {'test_basic[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nDEBUG cwltool:job.py:215 [job env3.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjmjn_h8g$ env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjmjn_h8g/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env3.cwl] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjmjn_h8g/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$966de77d2103268fd78d908121525434be2d0ad3",\n "size": 1226,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjvgv7c00\nDEBUG cwltool:job.py:454 [job env3.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryrtx9m3aw\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjmjn_h8g/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params0_0/canaryjmjn_h8g\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0007479509995391709 - start: 1685951408.8067641 - stop: 1685951408.807515 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_environment.py::test_basic[crt_params0] - location: ('tests/test_environment.py', 191, 'test_basic[crt_params0]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_environment.py::test_basic[crt_params1] - location: ('tests/test_environment.py', 191, 'test_basic[crt_params1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x104cdb9d0> [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_basic[crt_params1] - location: ('tests/test_environment.py', 191, 'test_basic[crt_params1]') - keywords: {'test_basic[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0013138579997757915 - start: 1685951408.8089118 - stop: 1685951408.8102279 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_basic[crt_params1] - location: ('tests/test_environment.py', 191, 'test_basic[crt_params1]') - keywords: {'test_basic[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job env3.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_2] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u,target=/hPkhbA \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryufjwpzr8,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryw6annf6u/20230605095011-660582.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/debian:stable-slim \\\n env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1\nINFO cwltool:job.py:905 [job env3.cwl_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job env3.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_2] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$025cbcc94e8ce3a391f3e8dff851c211a1819b4c",\n "size": 113,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_2] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryzd_f_z5e\nDEBUG cwltool:job.py:454 [job env3.cwl_2] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryufjwpzr8\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 3.873030120999829 - start: 1685951408.810559 - stop: 1685951412.6834931 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_basic[crt_params1] - location: ('tests/test_environment.py', 191, 'test_basic[crt_params1]') - keywords: {'test_basic[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job env3.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_2] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u,target=/hPkhbA \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryufjwpzr8,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryw6annf6u/20230605095011-660582.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/debian:stable-slim \\\n env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1\nINFO cwltool:job.py:905 [job env3.cwl_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job env3.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_2] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$025cbcc94e8ce3a391f3e8dff851c211a1819b4c",\n "size": 113,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_2] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryzd_f_z5e\nDEBUG cwltool:job.py:454 [job env3.cwl_2] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canaryufjwpzr8\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_basic_crt_params1_0/canarynhf6981u\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0006656190007561236 - start: 1685951412.684598 - stop: 1685951412.6852648 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_environment.py::test_basic[crt_params1] - location: ('tests/test_environment.py', 191, 'test_basic[crt_params1]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_environment.py::test_basic[crt_params2] - location: ('tests/test_environment.py', 191, 'test_basic[crt_params2]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_runtest_makereport [hook] - item: - call: > - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_basic[crt_params2] - location: ('tests/test_environment.py', 191, 'test_basic[crt_params2]') - keywords: {'test_basic[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: skipped - longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_environment.py', 192, 'Skipped: Requires the singularity executable on the system path.') - when: setup - user_properties: [] - sections: [] - duration: 0.0002027240007009823 - start: 1685951412.686377 - stop: 1685951412.68658 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_basic[crt_params2] - location: ('tests/test_environment.py', 191, 'test_basic[crt_params2]') - keywords: {'test_basic[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00015694499961682595 - start: 1685951412.68734 - stop: 1685951412.687498 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_environment.py::test_basic[crt_params2] - location: ('tests/test_environment.py', 191, 'test_basic[crt_params2]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params0] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params0]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x104a86740> [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params0] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params0]') - keywords: {'test_preserve_single[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0012861739996878896 - start: 1685951412.6882079 - stop: 1685951412.689495 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params0] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params0]') - keywords: {'test_preserve_single[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_3] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nDEBUG cwltool:job.py:215 [job env3.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_3] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf$ env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env3.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_3] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$98d334f5480b7a9c4903726f56fd4214268831dc",\n "size": 1255,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_3] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary_habet66\nDEBUG cwltool:job.py:454 [job env3.cwl_3] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary_jixfjk5\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.7478333760000169 - start: 1685951412.6898298 - stop: 1685951413.4376478 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params0] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params0]') - keywords: {'test_preserve_single[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_3] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nDEBUG cwltool:job.py:215 [job env3.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_3] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf$ env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env3.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_3] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$98d334f5480b7a9c4903726f56fd4214268831dc",\n "size": 1255,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_3] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary_habet66\nDEBUG cwltool:job.py:454 [job env3.cwl_3] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary_jixfjk5\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param0/canary73do21bf\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0005249089999779244 - start: 1685951413.438499 - stop: 1685951413.439025 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params0] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params0]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params1] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x104a86c80> [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params1] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params1]') - keywords: {'test_preserve_single[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0019601840003815596 - start: 1685951413.4402938 - stop: 1685951413.442256 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: [] [hook] - pytest_exception_interact [hook] - node: - call: > - report: - finish pytest_exception_interact --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10238f730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10238f730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_dependencies.py::test_biocontainers_resolution - location: ('tests/test_dependencies.py', 44, 'test_biocontainers_resolution') - keywords: {'test_biocontainers_resolution': 1, 'skipif': 1, 'pytestmark': 1, 'test_dependencies.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:11]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/seqtk_seq.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/seqtk_seq.cwl'\n"), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/seqtk_seq.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/seqtk_seq.cwl\'\nERROR galaxy.tool_util.deps.containers:containers.py:283 Could not get container description for tool \'None\'\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/containers.py", line 281, in find_best_container_description\n resolved_container_description = self.resolve(enabled_container_types, tool_info, **kwds)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/containers.py", line 303, in resolve\n container_description = container_resolver.resolve(enabled_container_types, tool_info, install=install, resolution_cache=resolution_cache, session=session)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/container_resolvers/mulled.py", line 465, in resolve\n return docker_cached_container_description(targets, self.namespace, hash_func=self.hash_func, shell=self.shell, resolution_cache=resolution_cache)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/container_resolvers/mulled.py", line 283, in docker_cached_container_description\n cached_images = list_docker_cached_mulled_images(namespace, hash_func=hash_func, resolution_cache=resolution_cache)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/container_resolvers/mulled.py", line 172, in list_docker_cached_mulled_images\n sorted_images = version_sorted([_ for _ in filter(name_filter, images_and_versions)])\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/mulled/util.py", line 185, in version_sorted\n elements = sorted(elements, key=lambda tag: tag.build_string, reverse=True)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/mulled/util.py", line 184, in \n elements = (parse_tag(tag) for tag in elements)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/galaxy/tool_util/deps/mulled/util.py", line 178, in parse_tag\n build_string=packaging.version.parse(build_string),\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/packaging/version.py", line 52, in parse\n return Version(version)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/packaging/version.py", line 198, in __init__\n raise InvalidVersion(f"Invalid version: \'{version}\'")\npackaging.version.InvalidVersion: Invalid version: \'pyhdfd78af_0\'')] - duration: 0.0005738190002375632 - start: 1685951411.163533 - stop: 1685951411.164108 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_dependencies.py::test_biocontainers_resolution - location: ('tests/test_dependencies.py', 44, 'test_biocontainers_resolution') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_dependencies.py::test_bioconda - location: ('tests/test_dependencies.py', 109, 'test_bioconda') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - early skip of rewriting module: galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages [assertion] - early skip of rewriting module: galaxy.tool_util.deps.resolvers.conda [assertion] - early skip of rewriting module: galaxy.tool_util.deps.resolvers.homebrew [assertion] - early skip of rewriting module: galaxy.tool_util.deps.resolvers.lmod [assertion] - early skip of rewriting module: galaxy.tool_util.deps.resolvers.modules [assertion] - early skip of rewriting module: galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages [assertion] - pytest_keyboard_interrupt [hook] - excinfo: - finish pytest_keyboard_interrupt --> [] [hook] - pytest_sessionfinish [hook] - session: testsfailed=2 testscollected=664> - exitstatus: 2 - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_sessionfinish --> [] [hook] - pytest_unconfigure [hook] - config: <_pytest.config.Config object at 0x10238f730> - finish pytest_unconfigure --> [] [hook] -DEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_4] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nWARNING cwltool:job.py:657 You have specified \'--preserve-environment={USEDVAR}\' while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility.\nDEBUG cwltool:job.py:215 [job env3.cwl_4] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_4] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez,target=/hPkhbA \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryx954o_yg,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canary5yh9uk_o/20230605095014-057454.cid \\\n --env=USEDVAR=VARVAL \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/debian:stable-slim \\\n env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez/1b478f4af38397731bf74573234c522d361a9eb1\nINFO cwltool:job.py:905 [job env3.cwl_4] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job env3.cwl_4] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_4] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$21616d2e4f8c7185153871c30db9a99dad652ccc",\n "size": 128,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_4] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryybs21h76\nDEBUG cwltool:job.py:454 [job env3.cwl_4] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryx954o_yg\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_single_crt_param1/canaryd_3pcfez\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0007345220001298003 - start: 1685951415.079991 - stop: 1685951415.080726 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params1] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params1]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params2] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params2]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_runtest_makereport [hook] - item: - call: > - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params2] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params2]') - keywords: {'test_preserve_single[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: skipped - longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_environment.py', 212, 'Skipped: Requires the singularity executable on the system path.') - when: setup - user_properties: [] - sections: [] - duration: 0.00021694799943361431 - start: 1685951415.081902 - stop: 1685951415.082119 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params2] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params2]') - keywords: {'test_preserve_single[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0001536189993203152 - start: 1685951415.0827148 - stop: 1685951415.08287 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_environment.py::test_preserve_single[crt_params2] - location: ('tests/test_environment.py', 211, 'test_preserve_single[crt_params2]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params0] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params0]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x104d16950> [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params0] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params0]') - keywords: {'test_preserve_all[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.001334257000053185 - start: 1685951415.083617 - stop: 1685951415.084952 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params0] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params0]') - keywords: {'test_preserve_all[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_5] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nDEBUG cwltool:job.py:215 [job env3.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44$ env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env3.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_5] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$58d270332a44ecf9d1615c2977eb9940c22dd22d",\n "size": 4123,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canaryp5usi8w2\nDEBUG cwltool:job.py:454 [job env3.cwl_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canarytlg76wbm\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.5813199350004652 - start: 1685951415.0852869 - stop: 1685951415.666594 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params0] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params0]') - keywords: {'test_preserve_all[crt_params0]': 1, 'parametrize': 1, 'pytestmark': 1, 'crt_params0': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_5] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nDEBUG cwltool:job.py:215 [job env3.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44$ env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env3.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_5] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$58d270332a44ecf9d1615c2977eb9940c22dd22d",\n "size": 4123,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canaryp5usi8w2\nDEBUG cwltool:job.py:454 [job env3.cwl_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canarytlg76wbm\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params0_0/canary8r0zjc44\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.000570821999644977 - start: 1685951415.6675022 - stop: 1685951415.668074 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params0] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params0]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params1] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x104d69ab0> [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params1] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params1]') - keywords: {'test_preserve_all[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0013532590000977507 - start: 1685951415.669211 - stop: 1685951415.6705651 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - pytest_assertrepr_compare [hook] - config: <_pytest.config.Config object at 0x1021af730> - op: == - left: /Users/jasperk/gitlab/cwltool/venv/bin:/Users/jasperk/.rd/bin:/usr/local/opt/ruby/bin:/Users/jasperk/Applications/Aspera CLI/bin:/usr/local/sbin:/Users/jasperk/mambaforge/bin:/Users/jasperk/mambaforge/condabin:/Users/jasperk/.sdkman/candidates/maven/current/bin:/Users/jasperk/.sdkman/candidates/java/current/bin:/Users/jasperk/.sdkman/candidates/gradle/current/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin://Applications/Topaz Photo AI.app/Contents/Resources/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Applications/COMETS:/Users/jasperk/.krew/bin - right: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin - finish pytest_assertrepr_compare --> [["'/Users/jaspe...erk/.krew/bin' == '/usr/local/s...in:/sbin:/bin'", '- /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', '+ /Users/jasperk/gitlab/cwltool/venv/bin:/Users/jasperk/.rd/bin:/usr/local/opt/ruby/bin:/Users/jasperk/Applications/Aspera CLI/bin:/usr/local/sbin:/Users/jasperk/mambaforge/bin:/Users/jasperk/mambaforge/condabin:/Users/jasperk/.sdkman/candidates/maven/current/bin:/Users/jasperk/.sdkman/candidates/java/current/bin:/Users/jasperk/.sdkman/candidates/gradle/current/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin://Applications/Topaz Photo AI.app/Contents/Resources/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Applications/COMETS:/Users/jasperk/.krew/bin']] [hook] - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params1] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params1]') - keywords: {'test_preserve_all[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nWARNING cwltool:job.py:657 You have specified \'--preserve-entire-environment\' while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility.\nDEBUG cwltool:job.py:215 [job env3.cwl_6] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_6] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek,target=/hPkhbA \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canary3h9ranb8,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canaryyk50isj1/20230605095016-345654.cid \\\n \'--env=PATH=/Users/jasperk/gitlab/cwltool/venv/bin:/Users/jasperk/.rd/bin:/usr/local/opt/ruby/bin:/Users/jasperk/Applications/Aspera CLI/bin:/usr/local/sbin:/Users/jasperk/mambaforge/bin:/Users/jasperk/mambaforge/condabin:/Users/jasperk/.sdkman/candidates/maven/current/bin:/Users/jasperk/.sdkman/candidates/java/current/bin:/Users/jasperk/.sdkman/candidates/gradle/current/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin://Applications/Topaz Photo AI.app/Contents/Resources/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Applications/COMETS:/Users/jasperk/.krew/bin\' \\\n --env=SDKMAN_VERSION=5.18.0 \\\n --env=yodaHost=data.yoda.wur.nl \\\n --env=CONDA_DEFAULT_ENV=base \\\n --env=CONDA_PYTHON_EXE=/Users/jasperk/mambaforge/bin/python \\\n --env=irodsZone=unlock \\\n \'--env=PS1=(venv) \' \\\n --env=CONDA_PREFIX=/Users/jasperk/mambaforge \\\n --env=MAVEN_HOME=/Users/jasperk/.sdkman/candidates/maven/current \\\n --env=yodaAuthScheme=password \\\n --env=yodaSSL=CS_NEG_REQUIRE \\\n --env=LD_LIBRARY_PATH=:/Library/gurobi912/mac64/lib/ \\\n --env=SDKMAN_DIR=/Users/jasperk/.sdkman \\\n --env=GUROBI_COMETS_HOME=/Library/gurobi912/mac64 \\\n --env=LOGNAME=jasperk \\\n --env=PWD=/Users/jasperk/gitlab/cwltool \\\n --env=yodaUserName=jasper.koehorst@wur.nl \\\n --env=PYCHARM_HOSTED=1 \\\n \'--env=PYTHONPATH=/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm:/Users/jasperk/gitlab/cwltool:/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm_matplotlib_backend:/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm_display\' \\\n --env=SHELL=/bin/zsh \\\n --env=PATH_TO_FX=/Applications/javafx-sdk-11.0.2/lib \\\n --env=PAGER=less \\\n --env=WURGITTOKEN=glpat-YvsgD4rxELQmW2KAT7jm \\\n --env=SDKMAN_CANDIDATES_API=https://api.sdkman.io/2 \\\n --env=OLDPWD=/ \\\n --env=ZSH=/Users/jasperk/.oh-my-zsh \\\n --env=TMPDIR=/tmp \\\n \'--env=PYCHARM_HELPERS_DIR=/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm\' \\\n --env=irodsHome=/unlock \\\n --env=VIRTUAL_ENV=/Users/jasperk/gitlab/cwltool/venv \\\n --env=XPC_FLAGS=0x0 \\\n --env=irodsAuthScheme=pam \\\n --env=yodaZone=unlock \\\n --env=yodaCwd=/ \\\n --env=__CF_USER_TEXT_ENCODING=0x1F5:0:0 \\\n --env=irodsCwd=/ \\\n \'--env=CONDA_PROMPT_MODIFIER=(base) \' \\\n --env=LESS=-R \\\n --env=LC_CTYPE=UTF-8 \\\n \'--env=MANPATH=/Users/jasperk/Applications/Aspera CLI/share/man:\' \\\n --env=CONDA_EXE=/Users/jasperk/mambaforge/bin/conda \\\n --env=JAVA_HOME=/Users/jasperk/.sdkman/candidates/java/current \\\n --env=yodaHome=/unlock \\\n --env=COMETS_HOME=/Applications/COMETS \\\n --env=COMMAND_MODE=unix2003 \\\n --env=GRADLE_HOME=/Users/jasperk/.sdkman/candidates/gradle/current \\\n --env=irodsSSL=CS_NEG_REQUIRE \\\n --env=_CE_M= \\\n --env=yodaPort=1247 \\\n --env=XPC_SERVICE_NAME=0 \\\n --env=irodsPort=1247 \\\n --env=CONDA_SHLVL=1 \\\n --env=PYCHARM_DISPLAY_PORT=63342 \\\n --env=SDKMAN_CANDIDATES_DIR=/Users/jasperk/.sdkman/candidates \\\n --env=__CFBundleIdentifier=com.jetbrains.pycharm \\\n --env=CPLEX_STUDIO_DIR221=/Applications/CPLEX_Studio221 \\\n --env=irodsPassword=AWMk9bG21DU94XeuKlYBOPbk881lLEswRMb9HKUUvFAc \\\n --env=LSCOLORS=Gxfxcxdxbxegedabagacad \\\n --env=PYTHONIOENCODING=UTF-8 \\\n --env=PYTEST_RUN_CONFIG=True \\\n --env=SDKMAN_PLATFORM=darwinx64 \\\n --env=USER=jasperk \\\n --env=PATH_TO_FX_MODS=/Applications/javafx-jmods-11.0.2 \\\n --env=yodaPassword=I8-vNP6E-xPE-QrVi85NFFCPuK7fnzbA \\\n --env=irodsUserName=jkoehorst \\\n --env=SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.Ye1Vp6eAdx/Listeners \\\n --env=_CE_CONDA= \\\n --env=PYTHONUNBUFFERED=1 \\\n --env=irodsHost=unlock-icat.irods.surfsara.nl \\\n --env=HOME=/hPkhbA \\\n --env=TEAMCITY_VERSION=LOCAL \\\n --env=_JB_PPRINT_PRIMITIVES=1 \\\n --env=PYTEST_XDIST_TESTRUNUID=ca4970838f1b415dbaafd06f56809891 \\\n --env=PYTEST_XDIST_WORKER=gw2 \\\n --env=PYTEST_XDIST_WORKER_COUNT=8 \\\n \'--env=PYTEST_CURRENT_TEST=tests/test_environment.py::test_preserve_all[crt_params1] (call)\' \\\n --env=USEDVAR=VARVAL \\\n --env=UNUSEDVAR=VARVAL \\\n docker.io/debian:stable-slim \\\n env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1\nINFO cwltool:job.py:905 [job env3.cwl_6] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job env3.cwl_6] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_6] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$89b13cb714abd50b411e8db5fae2226f9942b1aa",\n "size": 3874,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_6] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canaryqq_9yop0\nDEBUG cwltool:job.py:454 [job env3.cwl_6] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canary3h9ranb8\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 1.694537264000246 - start: 1685951415.6709042 - stop: 1685951417.3654 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params1] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params1]') - keywords: {'test_preserve_all[crt_params1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params1': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env3.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env3.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env3.cwl_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env3.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env3.cwl_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env3.cwl_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env3.cwl_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-0"\n }\n]\nWARNING cwltool:job.py:657 You have specified \'--preserve-entire-environment\' while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility.\nDEBUG cwltool:job.py:215 [job env3.cwl_6] initial work dir {}\nINFO cwltool:job.py:266 [job env3.cwl_6] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek,target=/hPkhbA \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canary3h9ranb8,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canaryyk50isj1/20230605095016-345654.cid \\\n \'--env=PATH=/Users/jasperk/gitlab/cwltool/venv/bin:/Users/jasperk/.rd/bin:/usr/local/opt/ruby/bin:/Users/jasperk/Applications/Aspera CLI/bin:/usr/local/sbin:/Users/jasperk/mambaforge/bin:/Users/jasperk/mambaforge/condabin:/Users/jasperk/.sdkman/candidates/maven/current/bin:/Users/jasperk/.sdkman/candidates/java/current/bin:/Users/jasperk/.sdkman/candidates/gradle/current/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin://Applications/Topaz Photo AI.app/Contents/Resources/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Users/jasperk/.local/bin:/Users/jasperk/Library/Python/3.8/bin:/Applications/COMETS:/Users/jasperk/.krew/bin\' \\\n --env=SDKMAN_VERSION=5.18.0 \\\n --env=yodaHost=data.yoda.wur.nl \\\n --env=CONDA_DEFAULT_ENV=base \\\n --env=CONDA_PYTHON_EXE=/Users/jasperk/mambaforge/bin/python \\\n --env=irodsZone=unlock \\\n \'--env=PS1=(venv) \' \\\n --env=CONDA_PREFIX=/Users/jasperk/mambaforge \\\n --env=MAVEN_HOME=/Users/jasperk/.sdkman/candidates/maven/current \\\n --env=yodaAuthScheme=password \\\n --env=yodaSSL=CS_NEG_REQUIRE \\\n --env=LD_LIBRARY_PATH=:/Library/gurobi912/mac64/lib/ \\\n --env=SDKMAN_DIR=/Users/jasperk/.sdkman \\\n --env=GUROBI_COMETS_HOME=/Library/gurobi912/mac64 \\\n --env=LOGNAME=jasperk \\\n --env=PWD=/Users/jasperk/gitlab/cwltool \\\n --env=yodaUserName=jasper.koehorst@wur.nl \\\n --env=PYCHARM_HOSTED=1 \\\n \'--env=PYTHONPATH=/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm:/Users/jasperk/gitlab/cwltool:/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm_matplotlib_backend:/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm_display\' \\\n --env=SHELL=/bin/zsh \\\n --env=PATH_TO_FX=/Applications/javafx-sdk-11.0.2/lib \\\n --env=PAGER=less \\\n --env=WURGITTOKEN=glpat-YvsgD4rxELQmW2KAT7jm \\\n --env=SDKMAN_CANDIDATES_API=https://api.sdkman.io/2 \\\n --env=OLDPWD=/ \\\n --env=ZSH=/Users/jasperk/.oh-my-zsh \\\n --env=TMPDIR=/tmp \\\n \'--env=PYCHARM_HELPERS_DIR=/Users/jasperk/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/231.9011.38/PyCharm.app/Contents/plugins/python/helpers/pycharm\' \\\n --env=irodsHome=/unlock \\\n --env=VIRTUAL_ENV=/Users/jasperk/gitlab/cwltool/venv \\\n --env=XPC_FLAGS=0x0 \\\n --env=irodsAuthScheme=pam \\\n --env=yodaZone=unlock \\\n --env=yodaCwd=/ \\\n --env=__CF_USER_TEXT_ENCODING=0x1F5:0:0 \\\n --env=irodsCwd=/ \\\n \'--env=CONDA_PROMPT_MODIFIER=(base) \' \\\n --env=LESS=-R \\\n --env=LC_CTYPE=UTF-8 \\\n \'--env=MANPATH=/Users/jasperk/Applications/Aspera CLI/share/man:\' \\\n --env=CONDA_EXE=/Users/jasperk/mambaforge/bin/conda \\\n --env=JAVA_HOME=/Users/jasperk/.sdkman/candidates/java/current \\\n --env=yodaHome=/unlock \\\n --env=COMETS_HOME=/Applications/COMETS \\\n --env=COMMAND_MODE=unix2003 \\\n --env=GRADLE_HOME=/Users/jasperk/.sdkman/candidates/gradle/current \\\n --env=irodsSSL=CS_NEG_REQUIRE \\\n --env=_CE_M= \\\n --env=yodaPort=1247 \\\n --env=XPC_SERVICE_NAME=0 \\\n --env=irodsPort=1247 \\\n --env=CONDA_SHLVL=1 \\\n --env=PYCHARM_DISPLAY_PORT=63342 \\\n --env=SDKMAN_CANDIDATES_DIR=/Users/jasperk/.sdkman/candidates \\\n --env=__CFBundleIdentifier=com.jetbrains.pycharm \\\n --env=CPLEX_STUDIO_DIR221=/Applications/CPLEX_Studio221 \\\n --env=irodsPassword=AWMk9bG21DU94XeuKlYBOPbk881lLEswRMb9HKUUvFAc \\\n --env=LSCOLORS=Gxfxcxdxbxegedabagacad \\\n --env=PYTHONIOENCODING=UTF-8 \\\n --env=PYTEST_RUN_CONFIG=True \\\n --env=SDKMAN_PLATFORM=darwinx64 \\\n --env=USER=jasperk \\\n --env=PATH_TO_FX_MODS=/Applications/javafx-jmods-11.0.2 \\\n --env=yodaPassword=I8-vNP6E-xPE-QrVi85NFFCPuK7fnzbA \\\n --env=irodsUserName=jkoehorst \\\n --env=SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.Ye1Vp6eAdx/Listeners \\\n --env=_CE_CONDA= \\\n --env=PYTHONUNBUFFERED=1 \\\n --env=irodsHost=unlock-icat.irods.surfsara.nl \\\n --env=HOME=/hPkhbA \\\n --env=TEAMCITY_VERSION=LOCAL \\\n --env=_JB_PPRINT_PRIMITIVES=1 \\\n --env=PYTEST_XDIST_TESTRUNUID=ca4970838f1b415dbaafd06f56809891 \\\n --env=PYTEST_XDIST_WORKER=gw2 \\\n --env=PYTEST_XDIST_WORKER_COUNT=8 \\\n \'--env=PYTEST_CURRENT_TEST=tests/test_environment.py::test_preserve_all[crt_params1] (call)\' \\\n --env=USEDVAR=VARVAL \\\n --env=UNUSEDVAR=VARVAL \\\n docker.io/debian:stable-slim \\\n env \\\n -0 > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1\nINFO cwltool:job.py:905 [job env3.cwl_6] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job env3.cwl_6] completed success\nDEBUG cwltool:job.py:422 [job env3.cwl_6] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1",\n "basename": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameroot": "1b478f4af38397731bf74573234c522d361a9eb1",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$89b13cb714abd50b411e8db5fae2226f9942b1aa",\n "size": 3874,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env3.cwl_6] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canaryqq_9yop0\nDEBUG cwltool:job.py:454 [job env3.cwl_6] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canary3h9ranb8\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek/1b478f4af38397731bf74573234c522d361a9eb1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/1b478f4af38397731bf74573234c522d361a9eb1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_preserve_all_crt_params1_0/canarymou7spek\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0005804459997307276 - start: 1685951417.366341 - stop: 1685951417.366923 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params1] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params1]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params2] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params2]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_runtest_makereport [hook] - item: - call: > - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params2] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params2]') - keywords: {'test_preserve_all[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: skipped - longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_environment.py', 236, 'Skipped: Requires the singularity executable on the system path.') - when: setup - user_properties: [] - sections: [] - duration: 0.00022360500042850617 - start: 1685951417.36818 - stop: 1685951417.368405 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params2] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params2]') - keywords: {'test_preserve_all[crt_params2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'crt_params2': 1, 'test_environment.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00018487499983166344 - start: 1685951417.369047 - stop: 1685951417.369233 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_environment.py::test_preserve_all[crt_params2] - location: ('tests/test_environment.py', 235, 'test_preserve_all[crt_params2]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo)-True]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> (foo) [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo)-True]') - keywords: {'test_expression_match[(foo)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0005319370002325741 - start: 1685951417.370126 - stop: 1685951417.370659 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo)-True]') - keywords: {'test_expression_match[(foo)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.0002729380003074766 - start: 1685951417.3710022 - stop: 1685951417.3712761 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish 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tests/test_examples.py::test_expression_match[(foo.bar)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar)-True]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> (foo.bar) [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo.bar)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar)-True]') - keywords: {'test_expression_match[(foo.bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0006095749995438382 - start: 1685951417.372681 - stop: 1685951417.373292 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo.bar)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar)-True]') - keywords: {'test_expression_match[(foo.bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.0006968730003791279 - start: 1685951417.374563 - stop: 1685951417.375263 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo.bar)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar)-True]') - keywords: {'test_expression_match[(foo.bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0004372200000943849 - start: 1685951417.375974 - stop: 1685951417.3764129 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo.bar)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar)-True]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'])-True]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> (foo['bar']) [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'])-True]") - keywords: {"test_expression_match[(foo['bar'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0004336890006015892 - start: 1685951417.377285 - stop: 1685951417.37772 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'])-True]") - keywords: {"test_expression_match[(foo['bar'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.0003180759995302651 - start: 1685951417.37807 - stop: 1685951417.378389 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'])-True]") - keywords: {"test_expression_match[(foo['bar'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00027549599963094806 - start: 1685951417.37879 - stop: 1685951417.379067 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'])-True]") - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo["bar"])-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo["bar"])-True]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> (foo["bar"]) [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo["bar"])-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo["bar"])-True]') - keywords: {'test_expression_match[(foo["bar"])-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo["bar"])-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0006303570007730741 - start: 1685951417.380036 - stop: 1685951417.380668 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo["bar"])-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo["bar"])-True]') - keywords: {'test_expression_match[(foo["bar"])-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo["bar"])-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.00030739700014237314 - start: 1685951417.381089 - stop: 1685951417.381397 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo["bar"])-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo["bar"])-True]') - keywords: {'test_expression_match[(foo["bar"])-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo["bar"])-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00042177999966952484 - start: 1685951417.381833 - stop: 1685951417.382256 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo["bar"])-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo["bar"])-True]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo.bar.baz)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar.baz)-True]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> (foo.bar.baz) [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo.bar.baz)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar.baz)-True]') - keywords: {'test_expression_match[(foo.bar.baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar.baz)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0004957529999956023 - start: 1685951417.383188 - stop: 1685951417.383685 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo.bar.baz)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar.baz)-True]') - keywords: {'test_expression_match[(foo.bar.baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar.baz)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.0003029549998245784 - start: 1685951417.3841019 - stop: 1685951417.384407 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo.bar.baz)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar.baz)-True]') - keywords: {'test_expression_match[(foo.bar.baz)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo.bar.baz)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0002607710002848762 - start: 1685951417.384783 - stop: 1685951417.385045 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo.bar.baz)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo.bar.baz)-True]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar'].baz)-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'].baz)-True]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> (foo['bar'].baz) [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar'].baz)-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'].baz)-True]") - keywords: {"test_expression_match[(foo['bar'].baz)-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'].baz)-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0004973000004611094 - start: 1685951417.385895 - stop: 1685951417.386393 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar'].baz)-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'].baz)-True]") - keywords: {"test_expression_match[(foo['bar'].baz)-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'].baz)-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.000273525000011432 - start: 1685951417.386875 - stop: 1685951417.387149 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar'].baz)-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'].baz)-True]") - keywords: {"test_expression_match[(foo['bar'].baz)-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar'].baz)-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0005088389998491039 - start: 1685951417.3877451 - stop: 1685951417.388255 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar'].baz)-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar'].baz)-True]") - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar']['baz'])-True]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> (foo['bar']['baz']) [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar']['baz'])-True]") - keywords: {"test_expression_match[(foo['bar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0005765379992226372 - start: 1685951417.389447 - stop: 1685951417.390026 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar']['baz'])-True]") - keywords: {"test_expression_match[(foo['bar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.0003066379995289026 - start: 1685951417.39059 - stop: 1685951417.390898 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar']['baz'])-True]") - keywords: {"test_expression_match[(foo['bar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['bar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00044312099998933263 - start: 1685951417.391335 - stop: 1685951417.3917801 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['bar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['bar']['baz'])-True]") - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['b\\'ar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b\\\\'ar']['baz'])-True]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> (foo['b\'ar']['baz']) [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['b\\'ar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b\\\\'ar']['baz'])-True]") - keywords: {"test_expression_match[(foo['b\\\\'ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b\\\\'ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00046658600058435695 - start: 1685951417.392732 - stop: 1685951417.3932002 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['b\\'ar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b\\\\'ar']['baz'])-True]") - keywords: {"test_expression_match[(foo['b\\\\'ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b\\\\'ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.00023022799996397225 - start: 1685951417.393606 - stop: 1685951417.393837 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['b\\'ar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b\\\\'ar']['baz'])-True]") - keywords: {"test_expression_match[(foo['b\\\\'ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b\\\\'ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00024392199975409312 - start: 1685951417.394188 - stop: 1685951417.394433 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['b\\'ar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b\\\\'ar']['baz'])-True]") - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['b ar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b ar']['baz'])-True]") - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> (foo['b ar']['baz']) [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['b ar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b ar']['baz'])-True]") - keywords: {"test_expression_match[(foo['b ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0006260029995246441 - start: 1685951417.395252 - stop: 1685951417.39588 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['b ar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b ar']['baz'])-True]") - keywords: {"test_expression_match[(foo['b ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.0003648389993031742 - start: 1685951417.396404 - stop: 1685951417.39677 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['b ar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b ar']['baz'])-True]") - keywords: {"test_expression_match[(foo['b ar']['baz'])-True]": 1, 'parametrize': 1, 'pytestmark': 1, "(foo['b ar']['baz'])-True": 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00047715800064906944 - start: 1685951417.397328 - stop: 1685951417.3978071 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo['b ar']['baz'])-True] - location: ('tests/test_examples.py', 64, "test_expression_match[(foo['b ar']['baz'])-True]") - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo_bar)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo_bar)-True]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> (foo_bar) [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo_bar)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo_bar)-True]') - keywords: {'test_expression_match[(foo_bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo_bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0005532409995794296 - start: 1685951417.399162 - stop: 1685951417.3997161 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo_bar)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo_bar)-True]') - keywords: {'test_expression_match[(foo_bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo_bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.00037115899976924993 - start: 1685951417.400146 - stop: 1685951417.400518 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_expression_match[(foo_bar)-True] - location: ('tests/test_examples.py', 64, 'test_expression_match[(foo_bar)-True]') - keywords: {'test_expression_match[(foo_bar)-True]': 1, 'parametrize': 1, 'pytestmark': 1, '(foo_bar)-True': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[]') - keywords: {'test_bad_basecommand_docker[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0006594790002054651 - start: 1685951416.980117 - stop: 1685951416.980778 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[]') - keywords: {'test_bad_basecommand_docker[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\ndocker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_5] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job missing-tool.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_5] /private/tmp/docker_tmpm4eqn0yg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpm4eqn0yg,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmphks0nyni,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmd8b5ps6/20230605095019-182844.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_5] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_5] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_5] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_5] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_5] Removing input staging directory /private/tmp/docker_tmp432ufbfz\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_5] Removing temporary directory /private/tmp/docker_tmphks0nyni\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm4eqn0yg\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] - duration: 3.219032992999928 - start: 1685951416.981208 - stop: 1685951420.2001631 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[]') - keywords: {'test_bad_basecommand_docker[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\ndocker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_5] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job missing-tool.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_5] /private/tmp/docker_tmpm4eqn0yg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpm4eqn0yg,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmphks0nyni,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmd8b5ps6/20230605095019-182844.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_5] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_5] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_5] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_5] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_5] Removing input staging directory /private/tmp/docker_tmp432ufbfz\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_5] Removing temporary directory /private/tmp/docker_tmphks0nyni\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm4eqn0yg\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] - duration: 0.0006168870004330529 - start: 1685951420.2012281 - stop: 1685951420.2018461 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> --parallel [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel]') - keywords: {'test_bad_basecommand_docker[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.000571511000089231 - start: 1685951420.2032309 - stop: 1685951420.203804 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel]') - keywords: {'test_bad_basecommand_docker[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(missing-tool.cwl_6), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job missing-tool.cwl_6] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_6] /private/tmp/docker_tmpgv0ryq66$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpgv0ryq66,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmpg4nxo9cz,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4n_ght97/20230605095020-930474.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_6] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_6] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_6] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_6] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_6] Removing input staging directory /private/tmp/docker_tmpsmvlejwl\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_6] Removing temporary directory /private/tmp/docker_tmpg4nxo9cz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpgv0ryq66\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] - duration: 1.7467867310006113 - start: 1685951420.204257 - stop: 1685951421.9510021 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel]') - keywords: {'test_bad_basecommand_docker[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(missing-tool.cwl_6), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job missing-tool.cwl_6] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_6] /private/tmp/docker_tmpgv0ryq66$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpgv0ryq66,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmpg4nxo9cz,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4n_ght97/20230605095020-930474.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_6] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_6] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_6] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_6] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_6] Removing input staging directory /private/tmp/docker_tmpsmvlejwl\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_6] Removing temporary directory /private/tmp/docker_tmpg4nxo9cz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpgv0ryq66\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] - duration: 0.0006506219997390872 - start: 1685951421.952221 - stop: 1685951421.952873 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--debug] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--debug]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> --debug [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--debug] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--debug]') - keywords: {'test_bad_basecommand_docker[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00046848400052112993 - start: 1685951421.954196 - stop: 1685951421.954665 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--debug] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--debug]') - keywords: {'test_bad_basecommand_docker[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_7] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:job.py:215 [job missing-tool.cwl_7] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_7] /private/tmp/docker_tmpdka9o_pd$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdka9o_pd,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmphj2qch10,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkmoolah4/20230605095022-719860.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_7] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_7] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_7] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_7] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_7] Removing input staging directory /private/tmp/docker_tmp1zqtff0b\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_7] Removing temporary directory /private/tmp/docker_tmphj2qch10\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdka9o_pd\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] - duration: 1.7834863939997376 - start: 1685951421.955127 - stop: 1685951423.73857 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--debug] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--debug]') - keywords: {'test_bad_basecommand_docker[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_7] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:job.py:215 [job missing-tool.cwl_7] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_7] /private/tmp/docker_tmpdka9o_pd$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdka9o_pd,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmphj2qch10,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkmoolah4/20230605095022-719860.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_7] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_7] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_7] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_7] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_7] Removing input staging directory /private/tmp/docker_tmp1zqtff0b\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_7] Removing temporary directory /private/tmp/docker_tmphj2qch10\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdka9o_pd\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] - duration: 0.0006310639992079814 - start: 1685951423.739579 - stop: 1685951423.740211 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--debug] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--debug]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel --debug] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel --debug]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> --parallel --debug [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel --debug] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel --debug]') - keywords: {'test_bad_basecommand_docker[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0008768999996391358 - start: 1685951423.742069 - stop: 1685951423.742949 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel --debug] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel --debug]') - keywords: {'test_bad_basecommand_docker[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_8] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(missing-tool.cwl_8), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job missing-tool.cwl_8] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_8] /private/tmp/docker_tmp7yjsr7dt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp7yjsr7dt,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmpfc4cbkyb,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpm_y03v2j/20230605095024-462520.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_8] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_8] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_8] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_8] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_8] Removing input staging directory /private/tmp/docker_tmpc4xsyrs6\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_8] Removing temporary directory /private/tmp/docker_tmpfc4cbkyb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7yjsr7dt\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] - duration: 1.7442920029998277 - start: 1685951423.743435 - stop: 1685951425.4876852 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel --debug] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel --debug]') - keywords: {'test_bad_basecommand_docker[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', 'docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "neenooGo": executable file not found in $PATH: unknown.\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job missing-tool.cwl_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/missing-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job missing-tool.cwl_8] {}\nDEBUG cwltool:command_line_tool.py:1000 [job missing-tool.cwl_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job missing-tool.cwl_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "neenooGo"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(missing-tool.cwl_8), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job missing-tool.cwl_8] initial work dir {}\nINFO cwltool:job.py:266 [job missing-tool.cwl_8] /private/tmp/docker_tmp7yjsr7dt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp7yjsr7dt,target=/qdtWBw \\\n --mount=type=bind,source=/private/tmp/docker_tmpfc4cbkyb,target=/tmp \\\n --workdir=/qdtWBw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpm_y03v2j/20230605095024-462520.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/qdtWBw \\\n docker.io/debian:stable-slim \\\n neenooGo\nINFO cwltool:job.py:905 [job missing-tool.cwl_8] Max memory used: 0MiB\nWARNING cwltool:job.py:369 [job missing-tool.cwl_8] exited with status: 127\nWARNING cwltool:job.py:417 [job missing-tool.cwl_8] completed permanentFail\nDEBUG cwltool:job.py:422 [job missing-tool.cwl_8] outputs {}\nDEBUG cwltool:job.py:446 [job missing-tool.cwl_8] Removing input staging directory /private/tmp/docker_tmpc4xsyrs6\nDEBUG cwltool:job.py:454 [job missing-tool.cwl_8] Removing temporary directory /private/tmp/docker_tmpfc4cbkyb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7yjsr7dt\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] - duration: 0.0006671000001006178 - start: 1685951425.488738 - stop: 1685951425.4894059 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_bad_basecommand_docker[--parallel --debug] - location: ('tests/test_examples.py', 1490, 'test_bad_basecommand_docker[--parallel --debug]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_v1_0_position_expression[] - location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_v1_0_position_expression[] - location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[]') - keywords: {'test_v1_0_position_expression[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0005782769994766568 - start: 1685951425.4908118 - stop: 1685951425.491391 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_v1_0_position_expression[] - location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[]') - keywords: {'test_v1_0_position_expression[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1090, in main\n loadingContext, uri = resolve_and_validate_document(\n File "/Users/jasperk/gitlab/cwltool/cwltool/load_tool.py", line 536, in resolve_and_validate_document\n validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/schema.py", line 407, in validate_doc\n raise ValidationException("", None, anyerrors, "*")\nschema_salad.exceptions.ValidationException: tests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int')] - duration: 0.7425466380000216 - start: 1685951425.491789 - stop: 1685951426.234318 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_v1_0_position_expression[] - location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[]') - keywords: {'test_v1_0_position_expression[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1090, in main\n loadingContext, uri = resolve_and_validate_document(\n File "/Users/jasperk/gitlab/cwltool/cwltool/load_tool.py", line 536, in resolve_and_validate_document\n validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/schema.py", line 407, in validate_doc\n raise ValidationException("", None, anyerrors, "*")\nschema_salad.exceptions.ValidationException: tests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int')] - duration: 0.00025266100055887364 - start: 1685951426.234826 - stop: 1685951426.23508 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_v1_0_position_expression[] - location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel] - location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> --parallel [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel] - location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel]') - keywords: {'test_v1_0_position_expression[--parallel]': 1, 'parametrize': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0003147369998259819 - start: 1685951426.235955 - stop: 1685951426.2362711 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel] - location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel]') - keywords: {'test_v1_0_position_expression[--parallel]': 1, 'parametrize': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1090, in main\n loadingContext, uri = resolve_and_validate_document(\n File "/Users/jasperk/gitlab/cwltool/cwltool/load_tool.py", line 536, in resolve_and_validate_document\n validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/schema.py", line 407, in validate_doc\n raise ValidationException("", None, anyerrors, "*")\nschema_salad.exceptions.ValidationException: tests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int')] - duration: 0.7869047670001237 - start: 1685951426.236619 - stop: 1685951427.023506 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel] - location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel]') - keywords: {'test_v1_0_position_expression[--parallel]': 1, 'parametrize': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[]') - keywords: {'test_cid_file_non_existing_dir[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _6] start\nDEBUG cwltool:workflow_job.py:777 [workflow _6] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _6] starting step task1_6\nDEBUG cwltool:workflow_job.py:727 [step task1_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_6] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_6\nDEBUG cwltool:command_line_tool.py:988 [job task1_5] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_5] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir0/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first')] - duration: 0.0011516250006025075 - start: 1685951426.511955 - stop: 1685951426.51311 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> --parallel [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel]') - keywords: {'test_cid_file_non_existing_dir[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0018225509993499145 - start: 1685951426.515224 - stop: 1685951426.517049 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel]') - keywords: {'test_cid_file_non_existing_dir[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step task1_7\nDEBUG cwltool:workflow_job.py:727 [step task1_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_7] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_7\nDEBUG cwltool:command_line_tool.py:988 [job task1_6] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_6), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _7] starting step task2_7\nDEBUG cwltool:workflow_job.py:727 [step task2_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_7] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_7\nDEBUG cwltool:command_line_tool.py:988 [job task2_5] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_6] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_5), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_5] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:executors.py:430 Workflow cannot make any more progress.\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmps3x313_o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpz8kgqzw8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmxatqzqe\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] - duration: 4.700235120999423 - start: 1685951426.517567 - stop: 1685951431.217685 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel]') - keywords: {'test_cid_file_non_existing_dir[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step task1_7\nDEBUG cwltool:workflow_job.py:727 [step task1_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_7] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_7\nDEBUG cwltool:command_line_tool.py:988 [job task1_6] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_6), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _7] starting step task2_7\nDEBUG cwltool:workflow_job.py:727 [step task2_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_7] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_7\nDEBUG cwltool:command_line_tool.py:988 [job task2_5] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_6] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_5), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_5] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir1/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:executors.py:430 Workflow cannot make any more progress.\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmps3x313_o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpz8kgqzw8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmxatqzqe\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] - duration: 0.0006869819999337778 - start: 1685951431.218774 - stop: 1685951431.219462 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--debug] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--debug]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir2 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir2 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> --debug [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--debug] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--debug]') - keywords: {'test_cid_file_non_existing_dir[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0018994199999724515 - start: 1685951431.2207181 - stop: 1685951431.2226188 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: [hook] - nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel --debug] - location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel --debug]') - keywords: {'test_v1_0_position_expression[--parallel --debug]': 1, 'parametrize': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-position-expr.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1090, in main\n loadingContext, uri = resolve_and_validate_document(\n File "/Users/jasperk/gitlab/cwltool/cwltool/load_tool.py", line 536, in resolve_and_validate_document\n validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/schema.py", line 407, in validate_doc\n raise ValidationException("", None, anyerrors, "*")\nschema_salad.exceptions.ValidationException: tests/echo-position-expr.cwl:3:1: Object \'tests/echo-position-expr.cwl\' is not valid because\n tried \'CommandLineTool\' but\ntests/echo-position-expr.cwl:7:1: * the \'inputs\' field is not valid because\ntests/echo-position-expr.cwl:8:3: item is invalid because\ntests/echo-position-expr.cwl:10:5: the \'inputBinding\' field is not valid because\n tried CommandLineBinding but\ntests/echo-position-expr.cwl:11:7: the \'position\' field is not valid because\n tried int but\n "\'$(self)\'" is not int\ntests/echo-position-expr.cwl:17:1: * the \'arguments\' field is not valid because\n tried array of but\ntests/echo-position-expr.cwl:18:5: item is invalid because\n tried CommandLineBinding but\n the \'position\' field is not valid because\n tried int but\n "\'${return 2;}\'" is not int')] - duration: 0.0002695859993764316 - start: 1685951428.471321 - stop: 1685951428.471591 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_v1_0_position_expression[--parallel --debug] - location: ('tests/test_examples.py', 1508, 'test_v1_0_position_expression[--parallel --debug]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--debug] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--debug]') - keywords: {'test_cid_file_non_existing_dir[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _8] start\nDEBUG cwltool:workflow_job.py:777 [workflow _8] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step task2_8\nDEBUG cwltool:workflow_job.py:727 [step task2_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_8] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_8] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_8\nDEBUG cwltool:command_line_tool.py:988 [job task2_6] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_6] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir2/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first')] - duration: 0.00091174199951638 - start: 1685951432.713697 - stop: 1685951432.7146099 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--debug] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--debug]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> --parallel --debug [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]') - keywords: {'test_cid_file_non_existing_dir[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0015594679998685024 - start: 1685951432.7161012 - stop: 1685951432.7176619 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]') - keywords: {'test_cid_file_non_existing_dir[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task2_9\nDEBUG cwltool:workflow_job.py:727 [step task2_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_9\nDEBUG cwltool:command_line_tool.py:988 [job task2_7] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_7), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task1_9\nDEBUG cwltool:workflow_job.py:727 [step task1_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_9\nDEBUG cwltool:command_line_tool.py:988 [job task1_7] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_7), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_7] initial work dir {}\nDEBUG cwltool:job.py:215 [job task1_7] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:executors.py:430 Workflow cannot make any more progress.\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcznvku2h\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwnjg_83y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa2g7ccv0\nWARNING cwltool:main.py:1364 Final process status is permanentFail')] - duration: 4.7696697329993185 - start: 1685951432.718051 - stop: 1685951437.487604 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]') - keywords: {'test_cid_file_non_existing_dir[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task2_9\nDEBUG cwltool:workflow_job.py:727 [step task2_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\n pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_ext.py::test_warn_large_inputs - location: ('tests/test_ext.py', 264, 'test_warn_large_inputs') - keywords: {'test_warn_large_inputs': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00031238300016411813 - start: 1685951436.9900942 - stop: 1685951436.990408 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_ext.py::test_warn_large_inputs - location: ('tests/test_ext.py', 264, 'test_warn_large_inputs') - keywords: {'test_warn_large_inputs': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{}'), ('Captured stderr call', '/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\'\nWARNING cwltool:process.py:795 tests/wf/listing_v1_0.cwl:5:3: Recursive directory listing has resulted in a large number of File\n objects (5) passed to the input parameter \'d\'. This may negatively\n affect workflow performance and memory use.\n \n If this is a problem, use the hint \'cwltool:LoadListingRequirement\'\n with "shallow_listing" or "no_listing" to change the directory\n listing behavior:\n \n $namespaces:\n cwltool: "http://commonwl.org/cwltool#"\n hints:\n cwltool:LoadListingRequirement:\n loadListing: shallow_listing\n \nDEBUG cwltool:command_line_tool.py:982 [job listing_v1_0.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\nDEBUG cwltool:command_line_tool.py:988 [job listing_v1_0.cwl] {\n "d": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4",\n "basename": "tmp4",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha",\n "basename": "alpha",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta",\n "basename": "delta",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot",\n "basename": "foxtrot",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo",\n "basename": "echo",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker",\n "basename": "baker",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie",\n "basename": "charlie",\n "size": 0\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job listing_v1_0.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4": [\n "/Users/jasperk/gitlab finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') - keywords: {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0016974030004348606 - start: 1685951437.491211 - stop: 1685951437.4929101 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') - keywords: {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task1_10\nDEBUG cwltool:workflow_job.py:727 [step task1_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_10\nDEBUG cwltool:command_line_tool.py:988 [job task1_8] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_8] initial work dir {}\nINFO cwltool:job.py:266 [job task1_8] /private/tmp/docker_tmpqd0zbt01$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqd0zbt01,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwbwvw4vq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095039-089090.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_8] completed success\nDEBUG cwltool:job.py:422 [job task1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqd0zbt01/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_10] completed success\nDEBUG cwltool:job.py:446 [job task1_8] Removing input staging directory /private/tmp/docker_tmpsuq2jbza\nDEBUG cwltool:job.py:454 [job task1_8] Removing temporary directory /private/tmp/docker_tmpwbwvw4vq\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task2_10\nDEBUG cwltool:workflow_job.py:727 [step task2_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_10\nDEBUG cwltool:command_line_tool.py:988 [job task2_8] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_8] initial work dir {}\nINFO cwltool:job.py:266 [job task2_8] /private/tmp/docker_tmpukxzzulb$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpukxzzulb,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp460y3fko,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095040-128027.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_8] completed success\nDEBUG cwltool:job.py:422 [job task2_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpukxzzulb/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_10] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {}\nDEBUG cwltool:job.py:446 [job task2_8] Removing input staging directory /private/tmp/docker_tmp0ewn2kda\nDEBUG cwltool:job.py:454 [job task2_8] Removing temporary directory /private/tmp/docker_tmp460y3fko\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpukxzzulb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqd0zbt01\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6qs7k1_4\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 3.6632841119999284 - start: 1685951437.4933639 - stop: 1685951441.156561 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') - keywords: {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task1_10\nDEBUG cwltool:workflow_job.py:727 [step task1_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_10\nDEBUG cwltool:command_line_tool.py:988 [job task1_8] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_8] initial work dir {}\nINFO cwltool:job.py:266 [job task1_8] /private/tmp/docker_tmpqd0zbt01$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqd0zbt01,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwbwvw4vq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095039-089090.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_8] completed success\nDEBUG cwltool:job.py:422 [job task1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqd0zbt01/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_10] completed success\nDEBUG cwltool:job.py:446 [job task1_8] Removing input staging directory /private/tmp/docker_tmpsuq2jbza\nDEBUG cwltool:job.py:454 [job task1_8] Removing temporary directory /private/tmp/docker_tmpwbwvw4vq\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task2_10\nDEBUG cwltool:workflow_job.py:727 [step task2_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_10\nDEBUG cwltool:command_line_tool.py:988 [job task2_8] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_8] initial work dir {}\nINFO cwltool:job.py:266 [job task2_8] /private/tmp/docker_tmpukxzzulb$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpukxzzulb,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp460y3fko,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095040-128027.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_8] completed success\nDEBUG cwltool:job.py:422 [job task2_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpukxzzulb/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_10] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {}\nDEBUG cwltool:job.py:446 [job task2_8] Removing input staging directory /private/tmp/docker_tmp0ewn2kda\nDEBUG cwltool:job.py:454 [job task2_8] Removing temporary directory /private/tmp/docker_tmp460y3fko\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpukxzzulb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqd0zbt01\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6qs7k1_4\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0008422430000791792 - start: 1685951441.1581 - stop: 1685951441.158945 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> --parallel [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') - keywords: {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0020675499999924796 - start: 1685951441.160426 - stop: 1685951441.162495 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') - keywords: {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_11\nDEBUG cwltool:workflow_job.py:727 [step task2_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_11\nDEBUG cwltool:command_line_tool.py:988 [job task2_9] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_9), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_11\nDEBUG cwltool:workflow_job.py:727 [step task1_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_11\nDEBUG cwltool:command_line_tool.py:988 [job task1_9] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_9] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_9), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task1_9] initial work dir {}\nINFO cwltool:job.py:266 [job task2_9] /private/tmp/docker_tmp6w_kuuwk$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp6w_kuuwk,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpimrbltf0,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-808365.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:266 [job task1_9] /private/tmp/docker_tmpqm8yecor$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqm8yecor,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpxft5vpeu,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-828561.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task2_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_9] completed success\nDEBUG cwltool:job.py:422 [job task2_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6w_kuuwk/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_11] completed success\nDEBUG cwltool:job.py:446 [job task2_9] Removing input staging directory /private/tmp/docker_tmpr2euvrmb\nDEBUG cwltool:job.py:454 [job task2_9] Removing temporary directory /private/tmp/docker_tmpimrbltf0\nINFO cwltool:job.py:905 [job task1_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_9] completed success\nDEBUG cwltool:job.py:422 [job task1_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqm8yecor/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_11] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_9] Removing input staging directory /private/tmp/docker_tmpfumwmmb0\nDEBUG cwltool:job.py:454 [job task1_9] Removing temporary directory /private/tmp/docker_tmpxft5vpeu\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqm8yecor\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp91c3ruq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6w_kuuwk\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 2.689709309999671 - start: 1685951441.163031 - stop: 1685951443.852674 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') - keywords: {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_11\nDEBUG cwltool:workflow_job.py:727 [step task2_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_11\nDEBUG cwltool:command_line_tool.py:988 [job task2_9] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_9), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_11\nDEBUG cwltool:workflow_job.py:727 [step task1_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_11\nDEBUG cwltool:command_line_tool.py:988 [job task1_9] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_9] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_9), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task1_9] initial work dir {}\nINFO cwltool:job.py:266 [job task2_9] /private/tmp/docker_tmp6w_kuuwk$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp6w_kuuwk,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpimrbltf0,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-808365.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:266 [job task1_9] /private/tmp/docker_tmpqm8yecor$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqm8yecor,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpxft5vpeu,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-828561.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task2_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_9] completed success\nDEBUG cwltool:job.py:422 [job task2_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6w_kuuwk/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_11] completed success\nDEBUG cwltool:job.py:446 [job task2_9] Removing input staging directory /private/tmp/docker_tmpr2euvrmb\nDEBUG cwltool:job.py:454 [job task2_9] Removing temporary directory /private/tmp/docker_tmpimrbltf0\nINFO cwltool:job.py:905 [job task1_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_9] completed success\nDEBUG cwltool:job.py:422 [job task1_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqm8yecor/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_11] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_9] Removing input staging directory /private/tmp/docker_tmpfumwmmb0\nDEBUG cwltool:job.py:454 [job task1_9] Removing temporary directory /private/tmp/docker_tmpxft5vpeu\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqm8yecor\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp91c3ruq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6w_kuuwk\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0007029949993011542 - start: 1685951443.85393 - stop: 1685951443.854634 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> --debug [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') - keywords: {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0021138760002941126 - start: 1685951443.8562508 - stop: 1685951443.858367 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') - keywords: {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task2_12\nDEBUG cwltool:workflow_job.py:727 [step task2_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_12\nDEBUG cwltool:command_line_tool.py:988 [job task2_10] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_10] initial work dir {}\nINFO cwltool:job.py:266 [job task2_10] /private/tmp/docker_tmp2edpsbck$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2edpsbck,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwpqrjecs,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095045-366456.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_10] completed success\nDEBUG cwltool:job.py:422 [job task2_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2edpsbck/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_12] completed success\nDEBUG cwltool:job.py:446 [job task2_10] Removing input staging directory /private/tmp/docker_tmpparyqua4\nDEBUG cwltool:job.py:454 [job task2_10] Removing temporary directory /private/tmp/docker_tmpwpqrjecs\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task1_12\nDEBUG cwltool:workflow_job.py:727 [step task1_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_12\nDEBUG cwltool:command_line_tool.py:988 [job task1_10] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_10] initial work dir {}\nINFO cwltool:job.py:266 [job task1_10] /private/tmp/docker_tmpl6uhq9ur$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpl6uhq9ur,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp3v2v_ylx,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095046-398112.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_10] completed success\nDEBUG cwltool:job.py:422 [job task1_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpl6uhq9ur/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_12] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {}\nDEBUG cwltool:job.py:446 [job task1_10] Removing input staging directory /private/tmp/docker_tmp7cq588zt\nDEBUG cwltool:job.py:454 [job task1_10] Removing temporary directory /private/tmp/docker_tmp3v2v_ylx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmbshxay5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpl6uhq9ur\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2edpsbck\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 3.559965896999529 - start: 1685951443.858878 - stop: 1685951447.418756 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') - keywords: {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task2_12\nDEBUG cwltool:workflow_job.py:727 [step task2_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_12\nDEBUG cwltool:command_line_tool.py:988 [job task2_10] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_10] initial work dir {}\nINFO cwltool:job.py:266 [job task2_10] /private/tmp/docker_tmp2edpsbck$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2edpsbck,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwpqrjecs,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095045-366456.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_10] completed success\nDEBUG cwltool:job.py:422 [job task2_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2edpsbck/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_12] completed success\nDEBUG cwltool:job.py:446 [job task2_10] Removing input staging directory /private/tmp/docker_tmpparyqua4\nDEBUG cwltool:job.py:454 [job task2_10] Removing temporary directory /private/tmp/docker_tmpwpqrjecs\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task1_12\nDEBUG cwltool:workflow_job.py:727 [step task1_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_12\nDEBUG cwltool:command_line_tool.py:988 [job task1_10] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_10] initial work dir {}\nINFO cwltool:job.py:266 [job task1_10] /private/tmp/docker_tmpl6uhq9ur$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpl6uhq9ur,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp3v2v_ylx,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095046-398112.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_10] completed success\nDEBUG cwltool:job.py:422 [job task1_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpl6uhq9ur/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_12] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {}\nDEBUG cwltool:job.py:446 [job task1_10] Removing input staging directory /private/tmp/docker_tmp7cq588zt\nDEBUG cwltool:job.py:454 [job task1_10] Removing temporary directory /private/tmp/docker_tmp3v2v_ylx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmbshxay5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpl6uhq9ur\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2edpsbck\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.000630780999927083 - start: 1685951447.419929 - stop: 1685951447.4205608 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> --parallel --debug [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') - keywords: {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0019516170004862943 - start: 1685951447.422921 - stop: 1685951447.424876 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') - keywords: {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task1_13\nDEBUG cwltool:workflow_job.py:727 [step task1_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_13\nDEBUG cwltool:command_line_tool.py:988 [job task1_11] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_11), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task2_13\nDEBUG cwltool:workflow_job.py:727 [step task2_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_13\nDEBUG cwltool:command_line_tool.py:988 [job task2_11] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_11] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_11), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_11] initial work dir {}\nINFO cwltool:job.py:266 [job task1_11] /private/tmp/docker_tmp4m9l14lt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp4m9l14lt,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpexenol_6,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-096004.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:266 [job task2_11] /private/tmp/docker_tmpq2su4gxh$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpq2su4gxh,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmplu6a4tzl,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-110322.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task1_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_11] completed success\nDEBUG cwltool:job.py:422 [job task1_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp4m9l14lt/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_13] completed success\nDEBUG cwltool:job.py:446 [job task1_11] Removing input staging directory /private/tmp/docker_tmpqp3usw7p\nDEBUG cwltool:job.py:454 [job task1_11] Removing temporary directory /private/tmp/docker_tmpexenol_6\nINFO cwltool:job.py:905 [job task2_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_11] completed success\nDEBUG cwltool:job.py:422 [job task2_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpq2su4gxh/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_13] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {}\nDEBUG cwltool:job.py:446 [job task2_11] Removing input staging directory /private/tmp/docker_tmp7r_dkuxt\nDEBUG cwltool:job.py:454 [job task2_11] Removing temporary directory /private/tmp/docker_tmplu6a4tzl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp4m9l14lt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzpg9e3kx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpq2su4gxh\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 2.7110078599998815 - start: 1685951447.425432 - stop: 1685951450.136374 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') - keywords: {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task1_13\nDEBUG cwltool:workflow_job.py:727 [step task1_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_13\nDEBUG cwltool:command_line_tool.py:988 [job task1_11] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_11), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task2_13\nDEBUG cwltool:workflow_job.py:727 [step task2_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_13\nDEBUG cwltool:command_line_tool.py:988 [job task2_11] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_11] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_11), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_11] initial work dir {}\nINFO cwltool:job.py:266 [job task1_11] /private/tmp/docker_tmp4m9l14lt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp4m9l14lt,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpexenol_6,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-096004.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:266 [job task2_11] /private/tmp/docker_tmpq2su4gxh$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpq2su4gxh,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmplu6a4tzl,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-110322.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task1_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_11] completed success\nDEBUG cwltool:job.py:422 [job task1_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp4m9l14lt/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_13] completed success\nDEBUG cwltool:job.py:446 [job task1_11] Removing input staging directory /private/tmp/docker_tmpqp3usw7p\nDEBUG cwltool:job.py:454 [job task1_11] Removing temporary directory /private/tmp/docker_tmpexenol_6\nINFO cwltool:job.py:905 [job task2_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_11] completed success\nDEBUG cwltool:job.py:422 [job task2_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpq2su4gxh/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_13] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {}\nDEBUG cwltool:job.py:446 [job task2_11] Removing input staging directory /private/tmp/docker_tmp7r_dkuxt\nDEBUG cwltool:job.py:454 [job task2_11] Removing temporary directory /private/tmp/docker_tmplu6a4tzl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp4m9l14lt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzpg9e3kx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpq2su4gxh\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0006579000000783708 - start: 1685951450.137392 - stop: 1685951450.138051 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> 그래프 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') - keywords: {'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0021395619996837922 - start: 1685951450.139597 - stop: 1685951450.141738 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') - keywords: {'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "그래프",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmplyn4vznq\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\nDEBUG cwltool:command_line_tool.py:988 [job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script] initial work dir {}\nINFO cwltool:job.py:266 [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script] completed success\nDEBUG cwltool:job.py:422 [job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\nDEBUG cwltool:job.py:454 [job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplyn4vznq\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.7623934020002707 - start: 1685951450.142199 - stop: 1685951450.9045749 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') - keywords: {'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "그래프",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmplyn4vznq\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\nDEBUG cwltool:command_line_tool.py:988 [job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script] initial work dir {}\nINFO cwltool:job.py:266 [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script] completed success\nDEBUG cwltool:job.py:422 [job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\nDEBUG cwltool:job.py:454 [job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplyn4vznq\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0008543869998902665 - start: 1685951450.9057658 - stop: 1685951450.906623 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> график [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') - keywords: {'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0022306440005195327 - start: 1685951450.908751 - stop: 1685951450.910984 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') - keywords: {'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "график",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp44oq2voa\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp44oq2voa\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.7918996069993227 - start: 1685951450.9114509 - stop: 1685951451.7033339 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') - keywords: {'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "график",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": 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"file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp44oq2voa\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp44oq2voa\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0011550549997991766 - start: 1685951451.705198 - stop: 1685951451.7063549 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> ð’ƒ [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') - keywords: {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0022639859998889733 - start: 1685951451.709167 - stop: 1685951451.711433 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') - keywords: {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/%F0%92%81%83",\n "basename": "ð’ƒ",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmppaqyosg7\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppaqyosg7\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.7048519689997192 - start: 1685951451.7120519 - stop: 1685951452.416888 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') - keywords: {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/%F0%92%81%83",\n "basename": "ð’ƒ",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmppaqyosg7\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppaqyosg7\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0006576920004590647 - start: 1685951452.418154 - stop: 1685951452.418813 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> ☕😠[hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') - keywords: {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0023664050004299497 - start: 1685951452.4210129 - stop: 1685951452.423381 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') - keywords: {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/%E2%98%95%F0%9F%98%8D",\n "basename": "☕ðŸ˜",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmptyp89s5l\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptyp89s5l\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.6462540919992534 - start: 1685951452.424056 - stop: 1685951453.070296 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') - keywords: {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/%E2%98%95%F0%9F%98%8D",\n "basename": "☕ðŸ˜",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmptyp89s5l\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptyp89s5l\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0006110310005169595 - start: 1685951453.071579 - stop: 1685951453.072191 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> امتحان [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') - keywords: {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0015628669998477562 - start: 1685951453.07393 - stop: 1685951453.0754938 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') - keywords: {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "امتحان",\n "class": "File",\n "checksum": 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{\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpu7fd0k2e\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu7fd0k2e\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.6586480109999684 - start: 1685951453.075871 - stop: 1685951453.734503 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') - keywords: {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "امتحان",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpu7fd0k2e\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu7fd0k2e\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0005586230008702842 - start: 1685951453.7356002 - stop: 1685951453.736159 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> abc+DEFGZ.z_12345- [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') - keywords: {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0013699379996978678 - start: 1685951453.7374332 - stop: 1685951453.7388039 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') - keywords: {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj2n4e2tf\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj2n4e2tf\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.6722589929995593 - start: 1685951453.739232 - stop: 1685951454.411476 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') - keywords: {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj2n4e2tf\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj2n4e2tf\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0010611549996610847 - start: 1685951454.412545 - stop: 1685951454.4136078 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names - location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_clt_returns_specialchar_n0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_clt_returns_specialchar_n0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names - location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') - keywords: {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.001187488999676134 - start: 1685951454.415158 - stop: 1685951454.416346 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names - location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') - keywords: {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.0065578280000408995 - start: 1685951454.416679 - stop: 1685951454.4232378 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names - location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') - keywords: {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0002504579997548717 - start: 1685951454.423627 - stop: 1685951454.423879 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names - location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: -expected1]> - pytest_runtest_logstart [hook] - nodeid: tests/test_pathmapper.py::test_subclass - location: ('tests/test_pathmapper.py', 8, 'test_subclass') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_pathmapper.py::test_subclass - location: ('tests/test_pathmapper.py', 8, 'test_subclass') - keywords: {'test_subclass': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00020675299947470194 - start: 1685951454.4253829 - stop: 1685951454.425591 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_pathmapper.py::test_subclass - location: ('tests/test_pathmapper.py', 8, 'test_subclass') - keywords: {'test_subclass': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.00025883699981932295 - start: 1685951454.4258912 - stop: 1685951454.4261508 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: -expected1]> - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw0/test_relocate_symlinks0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_relocate.py::test_relocate_symlinks - location: ('tests/test_relocate.py', 57, 'test_relocate_symlinks') - keywords: {'test_relocate_symlinks': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0011758240007111453 - start: 1685951453.878428 - stop: 1685951453.8796039 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_relocate.py::test_relocate_symlinks - location: ('tests/test_relocate.py', 57, 'test_relocate_symlinks') - keywords: {'test_relocate_symlinks': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{\n "bar": {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo",\n "basename": "foo",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\ntotal 0\nlrwxr-xr-x 1 jasperk wheel 46 Jun 5 09:50 dir2 -> /Users/jasperk/gitlab/cwltool/tests/reloc/dir2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmphfn_s4u0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\nDEBUG cwltool:command_line_tool.py:988 [job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job test.cwl] completed success\nDEBUG cwltool:job.py:422 [job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\nDEBUG cwltool:job.py:454 [job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmphfn_s4u0\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.7850257770005555 - start: 1685951453.879943 - stop: 1685951454.664951 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_relocate.py::test_relocate_symlinks - location: ('tests/test_relocate.py', 57, 'test_relocate_symlinks') - keywords: {'test_relocate_symlinks': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "bar": {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo",\n "basename": "foo",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\ntotal 0\nlrwxr-xr-x 1 jasperk wheel 46 Jun 5 09:50 dir2 -> /Users/jasperk/gitlab/cwltool/tests/reloc/dir2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmphfn_s4u0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\nDEBUG cwltool:command_line_tool.py:988 [job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job test.cwl] completed success\nDEBUG cwltool:job.py:422 [job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\nDEBUG cwltool:job.py:454 [job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmphfn_s4u0\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0007529229997089715 - start: 1685951454.666344 - stop: 1685951454.667098 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_relocate.py::test_relocate_symlinks - location: ('tests/test_relocate.py', 57, 'test_relocate_symlinks') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_schemadef.py::test_schemadef - location: ('tests/test_schemadef.py', 7, 'test_schemadef') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_schemadef.py::test_schemadef - location: ('tests/test_schemadef.py', 7, 'test_schemadef') - keywords: {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00033530900054756785 - start: 1685951454.669056 - stop: 1685951454.6693928 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_schemadef.py::test_schemadef - location: ('tests/test_schemadef.py', 7, 'test_schemadef') - keywords: {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard")] - duration: 14.348487793000459 - start: 1685951454.6698 - stop: 1685951469.017929 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_schemadef.py::test_schemadef - location: ('tests/test_schemadef.py', 7, 'test_schemadef') - keywords: {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard")] - duration: 0.0002445029995215009 - start: 1685951469.018733 - stop: 1685951469.018979 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_schemadef.py::test_schemadef - location: ('tests/test_schemadef.py', 7, 'test_schemadef') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: -hello bar]> - pytest_runtest_logstart [hook] - nodeid: tests/test_secrets.py::test_obscuring - location: ('tests/test_secrets.py', 24, 'test_obscuring') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> (, {'foo': '(secret-de0c4069-28c0-4d68-919d-2a178da99e07)', 'baz': 'quux'}) [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_secrets.py::test_obscuring - location: ('tests/test_secrets.py', 24, 'test_obscuring') - keywords: {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0003606910004236852 - start: 1685951469.0202398 - stop: 1685951469.020601 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_secrets.py::test_obscuring - location: ('tests/test_secrets.py', 24, 'test_obscuring') - keywords: {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.00022766500023863045 - start: 1685951469.020917 - stop: 1685951469.021145 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: -hello bar]> - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_secrets.py::test_obscuring - location: ('tests/test_secrets.py', 24, 'test_obscuring') - keywords: {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00021421099972940283 - start: 1685951469.021472 - stop: 1685951469.021687 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_secrets.py::test_obscuring - location: ('tests/test_secrets.py', 24, 'test_obscuring') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: -hello bar]> - nextitem: None - pytest_runtest_logstart [hook] - nodeid: tests/test_secrets.py::test_secrets[-hello bar] - location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: -hello bar]> - pytest_fixture_setup [hook] - fixturedef: - request: -hello bar]>> - finish pytest_fixture_setup --> at 0x10fa4a200> [hook] - pytest_fixture_setup [hook] - fixturedef: - request: -hello bar]>> - finish pytest_fixture_setup --> hello bar [hook] - pytest_fixture_setup [hook] - fixturedef: - request: -hello bar]>> - finish pytest_fixture_setup --> (, {'foo': '(secret-89826d56-2552-46d0-8c3c-1d800ae4b08f)', 'baz': 'quux'}) [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: -hello bar]> - call: - finish pytest_runtest_makereport --> -hello bar]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -hello bar]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: -hello bar]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: -hello bar]' when='setup' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_secrets.py::test_secrets[-hello bar] - location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') - keywords: {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0005970800002614851 - start: 1685951469.022847 - stop: 1685951469.023445 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: -hello bar]> - pytest_pyfunc_call [hook] - pyfuncitem: -hello bar]> - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: -hello bar]> - call: - finish pytest_runtest_makereport --> -hello bar]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -hello bar]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: -hello bar]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: -hello bar]' when='call' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_secrets.py::test_secrets[-hello bar] - location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') - keywords: {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.0002542570000514388 - start: 1685951469.023823 - stop: 1685951469.0240781 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: -hello bar]> - nextitem: None - pytest_fixture_post_finalizer [hook] - fixturedef: - request: -hello bar]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: -hello bar]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: -hello bar]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: -hello bar]> - call: - finish pytest_runtest_makereport --> -hello bar]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -hello bar]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: -hello bar]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - report: -hello bar]' when='teardown' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_secrets.py::test_secrets[-hello bar] - location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') - keywords: {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0006589340000573429 - start: 1685951469.0244741 - stop: 1685951469.025135 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_secrets.py::test_secrets[-hello bar] - location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - finish pytest_runtestloop --> True [hook] - pytest_sessionfinish [hook] - session: - exitstatus: 0 - finish pytest_sessionfinish --> [] [hook] - pytest_unconfigure [hook] - config: <_pytest.config.Config object at 0x10d3a7730> - finish pytest_unconfigure --> [] [hook] -e [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_no_output - location: ('tests/test_stdout_stderr_log_dir.py', 22, 'test_log_dir_echo_no_output') - keywords: {'test_log_dir_echo_no_output': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-stdout-log-dir.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": 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success\nDEBUG cwltool:job.py:422 [job echo] outputs {}\nDEBUG cwltool:job.py:446 [job echo] Removing input staging directory /private/tmp/docker_tmpcmod_263\nDEBUG cwltool:job.py:454 [job echo] Removing temporary directory /private/tmp/docker_tmpavw9i6k7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0vbn7hgf\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0005319940000845236 - start: 1685951459.2613251 - stop: 1685951459.261858 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_no_output - location: ('tests/test_stdout_stderr_log_dir.py', 22, 'test_log_dir_echo_no_output') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-False-True] - location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-False-True]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> False [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> True [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-False-True] - location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-False-True]') - keywords: {'test_input_can_be_named_pipe[True-False-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'True-False-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0015479650000997935 - start: 1685951459.263019 - stop: 1685951459.264568 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-False-True] - location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-False-True]') - keywords: {'test_input_can_be_named_pipe[True-False-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'True-False-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "streamable": true,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evgsqz7a/stg12438716-31e9-4e5e-870c-e991cb27f8a7/tmp",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\nDEBUG cwltool:command_line_tool.py:988 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "streamable": true,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_T0/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evgsqz7a/stg12438716-31e9-4e5e-870c-e991cb27f8a7/tmp",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] command line bindings is []')] - duration: 0.0068048149996684515 - start: 1685951459.2649379 - stop: 1685951459.271744 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-False-True] - location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-False-True]') - keywords: {'test_input_can_be_named_pipe[True-False-True]': 1, 'parametrize': 1, 'pytestmark': 1, 'True-False-True': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a] {\n "inp": {\n "class": "File",\n "location": 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pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] - location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') - keywords: {'test_subclass_CLT[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.004742043999613088 - start: 1685951459.296237 - stop: 1685951459.300981 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] - location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') - keywords: {'test_subclass_CLT[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0002549229993746849 - start: 1685951459.301441 - stop: 1685951459.301697 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] - location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1] - location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> [hook] - baseCommand: echo - class: CommandLineTool - cwlVersion: v1.0 - id: anon_enum_inside_array_inside_schemadef.cwl - inputs: [{'id': 'anon_enum_inside_array_inside_schemadef.cwl#first', 'type': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params'}] - outputs: [] - requirements: [{'class': 'SchemaDefRequirement', 'types': [{'fields': [{'name': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build', 'type': ['null', {'symbols': ['anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCh37', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCh38', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCm38'], 'type': 'enum'}]}, {'name': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species', 'type': ['null', {'symbols': ['anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species/homo_sapiens', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species/mus_musculus'], 'type': 'enum'}]}], 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0.00045941999997012317 - start: 1685951459.303957 - stop: 1685951459.3044171 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1] - location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]') - keywords: {'test_subclass_CLT[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.0067608899998958805 - start: 1685951459.304898 - stop: 1685951459.31166 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1] - location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]') - keywords: {'test_subclass_CLT[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00024648799990245607 - start: 1685951459.3120792 - stop: 1685951459.312327 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet1] - location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet1]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] - location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> [hook] - baseCommand: echo - class: CommandLineTool - cwlVersion: v1.0 - id: anon_enum_inside_array.cwl - inputs: [{'id': 'anon_enum_inside_array.cwl#first', 'type': {'fields': [{'name': 'anon_enum_inside_array.cwl#first/species', 'type': [{'symbols': ['anon_enum_inside_array.cwl#first/species/homo_sapiens', 'anon_enum_inside_array.cwl#first/species/mus_musculus'], 'type': 'enum'}, 'null']}], 'type': 'record'}}, {'id': 'anon_enum_inside_array.cwl#second', 'type': ['null', {'symbols': ['anon_enum_inside_array.cwl#second/homo_sapiens', 'anon_enum_inside_array.cwl#second/mus_musculus'], 'type': 'enum'}]}] - outputs: [] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] - location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') - keywords: {'test_subclass_exprtool[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0003593909996197908 - start: 1685951459.3131678 - stop: 1685951459.313528 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] - location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') - keywords: {'test_subclass_exprtool[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.004536303000350017 - start: 1685951459.313875 - stop: 1685951459.318412 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] - location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') - keywords: {'test_subclass_exprtool[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0002397010002823663 - start: 1685951459.318814 - stop: 1685951459.3190541 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet0] - location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet0]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] - location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> [hook] - baseCommand: echo - class: CommandLineTool - cwlVersion: v1.0 - id: anon_enum_inside_array_inside_schemadef.cwl - inputs: [{'id': 'anon_enum_inside_array_inside_schemadef.cwl#first', 'type': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params'}] - outputs: [] - requirements: [{'class': 'SchemaDefRequirement', 'types': [{'fields': [{'name': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build', 'type': ['null', {'symbols': ['anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCh37', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCh38', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/ncbi_build/GRCm38'], 'type': 'enum'}]}, {'name': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species', 'type': ['null', {'symbols': ['anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species/homo_sapiens', 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params/species/mus_musculus'], 'type': 'enum'}]}], 'name': 'anon_enum_inside_array_inside_schemadef.cwl#vcf2maf_params', 'type': 'record'}]}] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] - location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') - keywords: {'test_subclass_exprtool[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0003865159997076262 - start: 1685951459.3204029 - stop: 1685951459.32079 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] - location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') - keywords: {'test_subclass_exprtool[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.006563943999935873 - start: 1685951459.321141 - stop: 1685951459.327706 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] - location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') - keywords: {'test_subclass_exprtool[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00027535600020200945 - start: 1685951459.328183 - stop: 1685951459.328459 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] - location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints - location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints - location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') - keywords: {'test_single_process_inherit_reqshints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0013924539998697583 - start: 1685951459.329356 - stop: 1685951459.330749 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints - location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') - keywords: {'test_single_process_inherit_reqshints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp1rf1mf2r$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp1rf1mf2r/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1rf1mf2r/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmpay9r1t0o\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmptl9zl9t0\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1rf1mf2r/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1rf1mf2r\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.823703552000552 - start: 1685951459.3311412 - stop: 1685951460.154825 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints - location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') - keywords: {'test_single_process_inherit_reqshints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp1rf1mf2r$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp1rf1mf2r/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1rf1mf2r/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmpay9r1t0o\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmptl9zl9t0\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1rf1mf2r/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1rf1mf2r\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.000500224999996135 - start: 1685951460.15571 - stop: 1685951460.156211 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints - location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision - location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision - location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') - keywords: {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0018444249999447493 - start: 1685951460.158337 - stop: 1685951460.160183 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision - location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') - keywords: {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl_2] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl_2] /private/tmp/docker_tmp0rf0qbvp$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp0rf0qbvp/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp0rf0qbvp/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl_2] Removing input staging directory /private/tmp/docker_tmpun5mynhb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl_2] Removing temporary directory /private/tmp/docker_tmp2g3z32z6\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0rf0qbvp/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0rf0qbvp\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.9018843539997761 - start: 1685951460.1607418 - stop: 1685951461.062607 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision - location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') - keywords: {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl_2] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl_2] /private/tmp/docker_tmp0rf0qbvp$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp0rf0qbvp/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp0rf0qbvp/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl_2] Removing input staging directory /private/tmp/docker_tmpun5mynhb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl_2] Removing temporary directory /private/tmp/docker_tmp2g3z32z6\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0rf0qbvp/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0rf0qbvp\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0007875250003053225 - start: 1685951461.064188 - stop: 1685951461.064978 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision - location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision - location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision - location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') - keywords: {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0019690780000019004 - start: 1685951461.066408 - stop: 1685951461.068379 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision - location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') - keywords: {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmpug5wf1yr$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpug5wf1yr/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpug5wf1yr/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmpr2_osg12\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpdzs6emmt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpug5wf1yr/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpug5wf1yr\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 1.0924644189999526 - start: 1685951461.068767 - stop: 1685951462.161207 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision - location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') - keywords: {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmpug5wf1yr$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpug5wf1yr/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpug5wf1yr/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmpr2_osg12\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpdzs6emmt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpug5wf1yr/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpug5wf1yr\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.001123591000578017 - start: 1685951462.162127 - stop: 1685951462.163251 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision - location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints - location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints - location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') - keywords: {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.001528846999462985 - start: 1685951462.165597 - stop: 1685951462.1671271 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints - location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') - keywords: {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_no_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_no_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_no_env.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_no_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_no_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_no_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_no_env.cwl] /private/tmp/docker_tmpvp0cy1ef$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpvp0cy1ef/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_no_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_no_env.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpvp0cy1ef/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$ab5f2a9add5f54622dde555ac8ae9a3000e5ee0a",\n "size": 26,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_no_env.cwl] Removing input staging directory /private/tmp/docker_tmp3ef9ddmc\nDEBUG cwltool:job.py:454 [job env-tool2_no_env.cwl] Removing temporary directory /private/tmp/docker_tmp8ts5h8fu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvp0cy1ef/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvp0cy1ef\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.9118393700000524 - start: 1685951462.167519 - stop: 1685951463.079338 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints - location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') - keywords: {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_no_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_no_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_no_env.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_no_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_no_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_no_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_no_env.cwl] /private/tmp/docker_tmpvp0cy1ef$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpvp0cy1ef/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_no_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_no_env.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpvp0cy1ef/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$ab5f2a9add5f54622dde555ac8ae9a3000e5ee0a",\n "size": 26,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_no_env.cwl] Removing input staging directory /private/tmp/docker_tmp3ef9ddmc\nDEBUG cwltool:job.py:454 [job env-tool2_no_env.cwl] Removing temporary directory /private/tmp/docker_tmp8ts5h8fu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvp0cy1ef/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvp0cy1ef\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0006480779993580654 - start: 1685951463.08046 - stop: 1685951463.08111 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints - location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs - location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs - location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') - keywords: {'test_print_targets_embedded_sub_subwfs': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0003258949991504778 - start: 1685951463.0834339 - stop: 1685951463.083762 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs - location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') - keywords: {'test_print_targets_embedded_sub_subwfs': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:924 Input targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 step1 Output targets:\nINFO cwltool:main.py:924 step1 Input targets:\nINFO cwltool:main.py:933 step1 steps targets:\nINFO cwltool:main.py:924 step1/stepX Output targets:\nINFO cwltool:main.py:924 step1/stepX Input targets:\nINFO cwltool:main.py:933 step1/stepX steps targets:\nINFO cwltool:main.py:924 step1/stepX/stepY Output targets:\nINFO cwltool:main.py:924 step1/stepX/stepY Input targets:\nINFO cwltool:main.py:924 step1/stepZ Output targets:\nINFO cwltool:main.py:924 step1/stepZ Input targets:")] - duration: 1.4377574809996077 - start: 1685951463.084152 - stop: 1685951464.521875 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs - location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') - keywords: {'test_print_targets_embedded_sub_subwfs': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:924 Input targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 step1 Output targets:\nINFO cwltool:main.py:924 step1 Input targets:\nINFO cwltool:main.py:933 step1 steps targets:\nINFO cwltool:main.py:924 step1/stepX Output targets:\nINFO cwltool:main.py:924 step1/stepX Input targets:\nINFO cwltool:main.py:933 step1/stepX steps targets:\nINFO cwltool:main.py:924 step1/stepX/stepY Output targets:\nINFO cwltool:main.py:924 step1/stepX/stepY Input targets:\nINFO cwltool:main.py:924 step1/stepZ Output targets:\nINFO cwltool:main.py:924 step1/stepZ Input targets:")] - duration: 0.00038978599968686467 - start: 1685951464.522656 - stop: 1685951464.523047 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs - location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: ]> - pytest_runtest_logstart [hook] - nodeid: tests/test_target.py::test_target_packed - location: ('tests/test_target.py', 29, 'test_target_packed') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_target.py::test_target_packed - location: ('tests/test_target.py', 29, 'test_target_packed') - keywords: {'test_target_packed': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00031677999959356384 - start: 1685951464.524877 - stop: 1685951464.5251951 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_target.py::test_target_packed - location: ('tests/test_target.py', 29, 'test_target_packed') - keywords: {'test_target_packed': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#echo as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmp4ub_5xg8\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpqn2zozpb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxsls6qw3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplfi3vkzu\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 1.532981734000714 - start: 1685951464.525578 - stop: 1685951466.0585248 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: ]> - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_target.py::test_target_packed - location: ('tests/test_target.py', 29, 'test_target_packed') - keywords: {'test_target_packed': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#echo as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmp4ub_5xg8\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpqn2zozpb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxsls6qw3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplfi3vkzu\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0004789479999089963 - start: 1685951466.0598578 - stop: 1685951466.060338 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_target.py::test_target_packed - location: ('tests/test_target.py', 29, 'test_target_packed') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: ]> - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: ]> - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> boolean [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> -#!/usr/bin/env cwl-runner -cwlVersion: v1.0 -class: CommandLineTool -inputs: - - id: bdg - type: "boolean" -outputs: - - id: output - type: File - outputBinding: - glob: foo -baseCommand: - - echo - - "ff" -stdout: foo - [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> at 0x107ca9c60> [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: ]' when='setup' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') - keywords: {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.002468566999596078 - start: 1685951466.062423 - stop: 1685951466.064893 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: ]> - pytest_pyfunc_call [hook] - pyfuncitem: ]> - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: ]' when='call' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') - keywords: {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script\n [-h] --bdg [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --bdg\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'")] - duration: 0.6429743959997722 - start: 1685951466.065346 - stop: 1685951466.7083058 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: ]> - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: ]' when='teardown' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') - keywords: {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script\n [-h] --bdg [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --bdg\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'")] - duration: 0.00043712600017897785 - start: 1685951466.709005 - stop: 1685951466.709443 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> [] [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> ['/home/bart/cwl_test/test1'] [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') - keywords: {'test_argparse_append_with_default[job_order0-expected_values0]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order0-expected_values0': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0005423120001069037 - start: 1685951466.713546 - stop: 1685951466.7140899 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') - keywords: {'test_argparse_append_with_default[job_order0-expected_values0]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order0-expected_values0': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")] - duration: 0.9063059879999855 - start: 1685951466.7145128 - stop: 1685951467.6207979 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') - keywords: {'test_argparse_append_with_default[job_order0-expected_values0]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order0-expected_values0': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")] - duration: 0.00041723600043042097 - start: 1685951467.621684 - stop: 1685951467.622103 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: None - pytest_runtest_logstart [hook] - nodeid: tests/test_trs.py::test_workflow_trs_template - location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_trs.py::test_workflow_trs_template - location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') - keywords: {'test_workflow_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0004815839993170812 - start: 1685951467.624228 - stop: 1685951467.624712 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_trs.py::test_workflow_trs_template - location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') - keywords: {'test_workflow_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', 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1685951468.282669 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: None - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - 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pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105587730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105587730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_trs.py::test_workflow_trs_template - location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') - keywords: {'test_workflow_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\nINFO cwltool:load_tool.py:102 Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'")] - duration: 0.0025651939995441353 - start: 1685951468.283201 - stop: 1685951468.285768 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_trs.py::test_workflow_trs_template - location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - finish pytest_runtestloop --> True [hook] - pytest_sessionfinish [hook] - session: - exitstatus: 0 - finish pytest_sessionfinish --> [] [hook] - pytest_unconfigure [hook] - config: <_pytest.config.Config object at 0x105587730> - finish pytest_unconfigure --> [] [hook] -eq.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6nz6ufny/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmp4ckaad43\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpzyry0m08\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6nz6ufny/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6nz6ufny\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.843506232999971 - start: 1685951459.815787 - stop: 1685951460.659273 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_collision - location: ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision') - keywords: {'test_single_process_inherit_reqs_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmp6nz6ufny$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp6nz6ufny/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6nz6ufny/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmp4ckaad43\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpzyry0m08\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6nz6ufny/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6nz6ufny\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0006021980007062666 - start: 1685951460.660255 - stop: 1685951460.6608582 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_collision - location: ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision - location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision - location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') - keywords: {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0014790080003876938 - start: 1685951460.662613 - stop: 1685951460.664093 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision - location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') - keywords: {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initializing from _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c\nDEBUG cwltool:command_line_tool.py:988 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "valueFrom": "$(runtime.cores)"\n }\n]\nDEBUG cwltool:job.py:215 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initial work dir {}\nINFO cwltool:job.py:266 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] /private/tmp/docker_tmp0kfy0hx0$ echo \\\n 1 > /private/tmp/docker_tmp0kfy0hx0/cores.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] completed success\nDEBUG cwltool:job.py:422 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp0kfy0hx0/cores.txt",\n "basename": "cores.txt",\n "nameroot": "cores",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing input staging directory /private/tmp/docker_tmpy2q4uxic\nDEBUG cwltool:job.py:454 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing temporary directory /private/tmp/docker_tmp3u7l8gu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0kfy0hx0/cores.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1/cores.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0kfy0hx0\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 1.0293492290002177 - start: 1685951460.664522 - stop: 1685951461.693847 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision - location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') - keywords: {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initializing from _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c\nDEBUG cwltool:command_line_tool.py:988 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "valueFrom": "$(runtime.cores)"\n }\n]\nDEBUG cwltool:job.py:215 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initial work dir {}\nINFO cwltool:job.py:266 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] /private/tmp/docker_tmp0kfy0hx0$ echo \\\n 1 > /private/tmp/docker_tmp0kfy0hx0/cores.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] completed success\nDEBUG cwltool:job.py:422 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp0kfy0hx0/cores.txt",\n "basename": "cores.txt",\n "nameroot": "cores",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing input staging directory /private/tmp/docker_tmpy2q4uxic\nDEBUG cwltool:job.py:454 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing temporary directory /private/tmp/docker_tmp3u7l8gu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0kfy0hx0/cores.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1/cores.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0kfy0hx0\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0005337309994501993 - start: 1685951461.694844 - stop: 1685951461.69538 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision - location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out - location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out - location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') - keywords: {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0026018169992312323 - start: 1685951461.6975958 - stop: 1685951461.7001998 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out - location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') - keywords: {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmp_d17nob5$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp_d17nob5/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfmqmaczt\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7l3r954g\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_d17nob5/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnx7s_q9a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_d17nob5\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 1.0173719809999966 - start: 1685951461.700803 - stop: 1685951462.7181509 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out - location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') - keywords: {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmp_d17nob5$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp_d17nob5/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfmqmaczt\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7l3r954g\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_d17nob5/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnx7s_q9a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_d17nob5\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.00103417099944636 - start: 1685951462.723277 - stop: 1685951462.7243142 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out - location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit - location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit - location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') - keywords: {'test_print_targets_embedded_reqsinherit': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00034795999999914784 - start: 1685951462.72735 - stop: 1685951462.727699 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit - location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') - keywords: {'test_print_targets_embedded_reqsinherit': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/double-nested.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/double-nested.cwl'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 compile Output targets:\nINFO cwltool:main.py:924 compile Input targets:\nINFO cwltool:main.py:933 compile steps targets:\nINFO cwltool:main.py:924 compile/nested_compile Output targets:\nINFO cwltool:main.py:924 compile/nested_compile Input targets:\nINFO cwltool:main.py:933 compile/nested_compile steps targets:\nINFO cwltool:main.py:924 compile/nested_compile/argument Output targets:\nINFO cwltool:main.py:924 compile/nested_compile/argument Input targets:\nINFO cwltool:main.py:924 compile/nested_compile/untar Output targets:\nINFO cwltool:main.py:924 compile/nested_compile/untar Input targets:\nINFO cwltool:main.py:924 create-tar Output targets:")] - duration: 1.7800267129996428 - start: 1685951462.728148 - stop: 1685951464.508131 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit - location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') - keywords: {'test_print_targets_embedded_reqsinherit': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/double-nested.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/double-nested.cwl'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 compile Output targets:\nINFO cwltool:main.py:924 compile Input targets:\nINFO cwltool:main.py:933 compile steps targets:\nINFO cwltool:main.py:924 compile/nested_compile Output targets:\nINFO cwltool:main.py:924 compile/nested_compile Input targets:\nINFO cwltool:main.py:933 compile/nested_compile steps targets:\nINFO cwltool:main.py:924 compile/nested_compile/argument Output targets:\nINFO cwltool:main.py:924 compile/nested_compile/argument Input targets:\nINFO cwltool:main.py:924 compile/nested_compile/untar Output targets:\nINFO cwltool:main.py:924 compile/nested_compile/untar Input targets:\nINFO cwltool:main.py:924 create-tar Output targets:")] - duration: 0.0002299979996678303 - start: 1685951464.5087712 - stop: 1685951464.509002 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit - location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: ]> - pytest_runtest_logstart [hook] - nodeid: tests/test_target.py::test_wrong_target - location: ('tests/test_target.py', 12, 'test_wrong_target') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_target.py::test_wrong_target - location: ('tests/test_target.py', 12, 'test_wrong_target') - keywords: {'test_wrong_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00020157000017206883 - start: 1685951464.510966 - stop: 1685951464.511168 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_target.py::test_wrong_target - location: ('tests/test_target.py', 12, 'test_wrong_target') - keywords: {'test_wrong_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mI'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\nERROR cwltool:main.py:1218 I'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'")] - duration: 1.5277158919998328 - start: 1685951464.511601 - stop: 1685951466.0392802 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: ]> - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_target.py::test_wrong_target - location: ('tests/test_target.py', 12, 'test_wrong_target') - keywords: {'test_wrong_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mI'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\nERROR cwltool:main.py:1218 I'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'")] - duration: 0.00023238100038724951 - start: 1685951466.039777 - stop: 1685951466.040011 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_target.py::test_wrong_target - location: ('tests/test_target.py', 12, 'test_wrong_target') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: ]> - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: ]> - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> help [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> -#!/usr/bin/env cwl-runner -cwlVersion: v1.0 -class: CommandLineTool -doc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)" -inputs: - #Give it a list of input files - - id: input - type: File - inputBinding: - position: 0 -outputs: - - id: output - type: File - outputBinding: - glob: test.txt -stdout: test.txt -baseCommand: [cat] - [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> at 0x1048b93f0> [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: ]' when='setup' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') - keywords: {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0021708399999624817 - start: 1685951466.04311 - stop: 1685951466.0452821 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: ]> - pytest_pyfunc_call [hook] - pyfuncitem: ]> - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: ]' when='call' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') - keywords: {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjo7d5ug0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_9] initial work dir {}\nINFO cwltool:job.py:266 [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_9] completed success\nDEBUG cwltool:job.py:422 [job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\nDEBUG cwltool:job.py:454 [job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjo7d5ug0\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.6606748949998291 - start: 1685951466.046178 - stop: 1685951466.70684 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: ]> - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: ]' when='teardown' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') - keywords: {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjo7d5ug0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_9] initial work dir {}\nINFO cwltool:job.py:266 [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_9] completed success\nDEBUG cwltool:job.py:422 [job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\nDEBUG cwltool:job.py:454 [job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjo7d5ug0\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0010807290000229841 - start: 1685951466.7084632 - stop: 1685951466.709545 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparser_without_doc - location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparser_without_doc - location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') - keywords: {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00038347800000337884 - start: 1685951466.7141151 - stop: 1685951466.7145011 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparser_without_doc - location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') - keywords: {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'")] - duration: 0.019146607000038784 - start: 1685951466.715123 - stop: 1685951466.734271 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1021af730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1021af730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparser_without_doc - location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') - keywords: {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'")] - duration: 0.00028543000007630326 - start: 1685951466.734833 - stop: 1685951466.7351198 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparser_without_doc - 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pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') - keywords: {'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: 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"/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script",\n "foo": {\n "one": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n },\n "two": "test"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsxld0jq6\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.6780413209999097 - start: 1685951465.1225579 - stop: 1685951465.8005838 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: ]> - nextitem: ]> - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: ]' when='teardown' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') - keywords: {'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '"test"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script",\n "foo": {\n "one": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n },\n "two": "test"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpsxld0jq6\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_c__n___0/script",\n "foo": {\n "one": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n },\n "two": "test"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsxld0jq6\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0005465860003823764 - start: 1685951465.8011048 - stop: 1685951465.801653 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: ]> - nextitem: ]> - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: ]> - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> foo with d [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> -#!/usr/bin/env cwl-runner - -cwlVersion: v1.0 -class: ExpressionTool - -inputs: - foo: - type: - - type: enum - symbols: [cymbal1, cymbal2] - -expression: $(inputs.foo) - -outputs: [] - [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> at 0x107ea1e10> [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: ]' when='setup' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') - keywords: {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.003713201000209665 - start: 1685951465.804359 - stop: 1685951465.808074 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: ]> - pytest_pyfunc_call [hook] - pyfuncitem: ]> - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: ]' when='call' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') - keywords: {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '"cymbal2"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpqi4cps3i\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqi4cps3i\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.714671594999345 - start: 1685951465.808789 - stop: 1685951466.523444 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: ]> - nextitem: ]> - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: ]' when='teardown' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') - keywords: {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '"cymbal2"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpqi4cps3i\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqi4cps3i\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.000832688000627968 - start: 1685951466.5242019 - stop: 1685951466.525036 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: ]> - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: ]> - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> foo with e [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> -#!/usr/bin/env cwl-runner - -cwlVersion: v1.0 -class: ExpressionTool - -inputs: - foo: File - -expression: '{"bar": $(inputs.foo.location)}' - -outputs: [] - [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> at 0x107ea1ea0> [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: ]' when='setup' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') - keywords: {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0017929050000020652 - start: 1685951466.527004 - stop: 1685951466.5287979 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: ]> - pytest_pyfunc_call [hook] - pyfuncitem: ]> - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: ]' when='call' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') - keywords: {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '"{\\"bar\\": http://example.com}"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjyzejhiw\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjyzejhiw\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.7014808530002483 - start: 1685951466.5291898 - stop: 1685951467.230655 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: ]> - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: ]' when='teardown' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') - keywords: {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '"{\\"bar\\": http://example.com}"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjyzejhiw\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjyzejhiw\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0005410029998529353 - start: 1685951467.23134 - stop: 1685951467.231882 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_trs.py::test_tool_trs_template - location: ('tests/test_trs.py', 93, 'test_tool_trs_template') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_trs.py::test_tool_trs_template - location: ('tests/test_trs.py', 93, 'test_tool_trs_template') - keywords: {'test_tool_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00025567400007275864 - start: 1685951467.234224 - stop: 1685951467.2344801 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_trs.py::test_tool_trs_template - location: ('tests/test_trs.py', 93, 'test_tool_trs_template') - keywords: {'test_tool_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\nINFO cwltool:load_tool.py:102 Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'")] - duration: 0.6917008549999082 - start: 1685951467.234879 - stop: 1685951467.9265652 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_trs.py::test_tool_trs_template - location: ('tests/test_trs.py', 93, 'test_tool_trs_template') - keywords: {'test_tool_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\nINFO cwltool:load_tool.py:102 Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'")] - duration: 0.00021415700030047446 - start: 1685951467.9271948 - stop: 1685951467.92741 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_trs.py::test_tool_trs_template - location: ('tests/test_trs.py', 93, 'test_tool_trs_template') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: None - pytest_runtest_logstart [hook] - nodeid: tests/test_validate_js.py::test_js_hint_basic - location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_js_hint_basic - location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') - keywords: {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0002251839996461058 - start: 1685951467.929321 - stop: 1685951467.929547 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_js_hint_basic - location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') - keywords: {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.010393084999122948 - start: 1685951467.930013 - stop: 1685951467.940408 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: None - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x105763730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x105763730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_js_hint_basic - location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') - keywords: {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0015349340001193923 - start: 1685951467.940873 - stop: 1685951467.942409 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_validate_js.py::test_js_hint_basic - location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - finish pytest_runtestloop --> True [hook] - pytest_sessionfinish [hook] - session: - exitstatus: 0 - finish pytest_sessionfinish --> [] [hook] - pytest_unconfigure [hook] - config: <_pytest.config.Config object at 0x105763730> - finish pytest_unconfigure --> [] [hook] -943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}, \'reverse_sort\': True}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b9792322151224743947536605dc9cca24e185d8 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 0b54605194d27895bfbccb163d89b64dba40161d9771e915b204ef89c0501446 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 924e606ff3341e4daea625839633159c1a0c71d12d64532f78160aa03284c5537f3726613c5fa3ec938e0cb3972113e20f4fde6617c88cc98f7e6ec6001e31b5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n },\n "reverse_sort": true\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step rev\nDEBUG cwltool:workflow_job.py:727 [step rev] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step rev] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step rev] start\nDEBUG cwltool:command_line_tool.py:982 [job rev] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/revtool.cwl as part of step rev\nDEBUG cwltool:command_line_tool.py:988 [job rev] {\n "revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job rev] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job rev] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "revtool_input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "dirname": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job rev] initial work dir {}\nINFO cwltool:job.py:266 [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:job.py:905 [job rev] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 97fe1b50b4582cebc7d853796ebd62e3e163aa3f data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nINFO cwltool:job.py:419 [job rev] completed success\nDEBUG cwltool:job.py:422 [job rev] outputs {\n "revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step rev] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:572 [step rev] completed success\nDEBUG cwltool:job.py:446 [job rev] Removing input staging directory /private/tmp/docker_tmp0onaxo3l\nDEBUG cwltool:job.py:454 [job rev] Removing temporary directory /private/tmp/docker_tmpwl097n7z\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step sorted\nDEBUG cwltool:workflow_job.py:727 [step sorted] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step sorted] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:75 [step sorted] start\nDEBUG cwltool:command_line_tool.py:982 [job sorted] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sorttool.cwl as part of step sorted\nDEBUG cwltool:command_line_tool.py:988 [job sorted] {\n "reverse": true,\n "sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job sorted] path mappings is {\n "file:///private/tmp/docker_tmpo8j3qsh0/output.txt": [\n "/private/tmp/docker_tmpo8j3qsh0/output.txt",\n "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job sorted] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sort"\n },\n {\n "position": [\n 1,\n "reverse"\n ],\n "prefix": "--reverse",\n "datum": true\n },\n {\n "position": [\n 2,\n "sorted_input"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1",\n "path": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "dirname": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job sorted] initial work dir {}\nINFO cwltool:job.py:266 [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\nINFO cwltool:job.py:905 [job sorted] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: b9214658cc453331b62c2282b772a5c063dbd284 data/b9/b9214658cc453331b62c2282b772a5c063dbd284\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nINFO cwltool:job.py:419 [job sorted] completed success\nDEBUG cwltool:job.py:422 [job sorted] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step sorted] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step sorted] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:job.py:446 [job sorted] Removing input staging directory /private/tmp/docker_tmpt9i2u3d_\nDEBUG cwltool:job.py:454 [job sorted] Removing temporary directory /private/tmp/docker_tmp7ypgmrbr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplkmwaaf_/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplkmwaaf_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp46e4pq4y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo8j3qsh0\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: df915edbd6b5e75857277eb6c8e1377f0d051ef1 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4e56225fad8da955eebc34f2c094def00b9a7b6b39c500bd4ba036618c22e6f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 42a067ea2914371f209f8c25161dee0d1589e739c64f3275519f23d0af480afc636ea8b3298663632e89b2033c18a855ad9eb5290298ed00837688a946ac1523 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 553157706bf95e14c524a396a623d0f3f87f8ecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c6eccb1bc96bd4f55d03be6f4c0262a736dd8296ecae60d0d403bc9bfc8ca92b metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: f8c2586c8f0749fe5ef9e772f752c63acc2ba9dc8176e2cd8da9e677b952f7ba5a8410f062937ee19a3db25b2a414ef3566294dec7e6b6d011f21d176f3e4e3f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: ca44d2cee82bdf4159a998516a8b7d97de4becde metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 9abbc3a964398906a0a6c446f05be412b4f818c5df80213eefb95585644407f9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4dd04bc545f060056ec3c0eb38c22e70e30c30f4b3d633c60a802e4fcb4607737e7938f57b1eaea5a7044b23bf39461a15ccd68a344564b0a257cb7c966d8562 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b52bb0536caa8678dee76e093bab66c9f6ab72d8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fe046d6822ede74b785f00faa9e38aeeb92d573926c5e8f0dc3e87ddcf655336 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 3fe06b96dca53c5afed7eee93e58b27dd8330c34ce5436271af797259e4ffbc9790bb32f8cdab7244e1a83d0f8f1137464dc0dd757d841ac69412932cf09a9f9 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e58bcf95cb06e3d42132d9c488c389eb62de0170 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 27f34aff0b66f02249b46599489c42e37efc5de28e05274bba403a11a31bd86e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4f70440a6e4c80363471248e4d36d4df1a61f6bdeebdc41391bab98dcc5715361142776d4dd4dcc2b9f81d4687b83ea3a259c4a52374d0e6bed988bb6cfc8683 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: bb4d8f1c88da465df4d205fe71778cf5ee0c971e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 45e8790efb18825deb4c136d97032976f831b167076b31e43bd6ae66fc7466d7 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: bad9c61094a072702da2befe78c06dc406039eba8d4f5abeb39fb0646589428829d6e32ce91b705be4d0b9eba94cad5ca02e0665a23e9190438ef61b05611244 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'sorted_output\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 0536da382206c737b78578fb4cd56d470854cb65 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: ca8f0addfb91188dc24d6f6f2455b58ba794fa05417a99e239993ca8a25627c4 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 1ecd7b38f4685c4c7c7a124deaf30613ef849999f7aa5afb3b537d294a9e66933052c4e35fcb2d7a37e565e33a918c497349b9fc901cf828c5f9cd592dce1114 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: eac590a030efa84e4abe5c70bfbbe059d59cb909 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c85344af5e84a113da5636b4c42935c478fe1b587b2f84f82aa07465a71ce1d1 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fc05d8795084ee56e93edfd135c625c462e71dfaed99a7dc613264eb2b8a75a518580a187fb580fa9309c4cb1398a6501040c6251a221f31cbe67c5576a5d799 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: a7199d53b1f707ab9bfa7a88f832a843a05da1b5 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 44dad89d06c949f171fb43e2c2a870f92520a7d288460cafadfd19afefb7697c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fed9bf631358efdec9cb96154215b41a76dc6b7cd38eeb794f6a94212e5fcf868dcc776b0cec9d950de8370d3e4399a7c36833da2d5bdebfb0e193d813047ad4 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 825bbdb1ae0c5b4dab6115409f478fd2b7546ef1 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 65c5c5444143e944a90a7ec7fed5e89f3b4195f53a84f0747bca4875ad8602ec bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 9212abe820053e53692266203ba3819ceae75bb7f5d82f74281d7d1e9e0682ee506d9b210ef2d2bae5396e8d0f751bafbdf1f361747bf3cdc4d9aaa247919f25 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance')] - duration: 4.937757239000348 - start: 1685951453.6408331 - stop: 1685951458.578468 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_revsort_workflow - location: ('tests/test_provenance.py', 74, 'test_revsort_workflow') - keywords: {'test_revsort_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "sorted_output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt",\n "basename": "output.txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step rev\n\x1b[1;30mINFO\x1b[0m [step rev] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\n\x1b[1;30mINFO\x1b[0m [job rev] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job rev] completed success\n\x1b[1;30mINFO\x1b[0m [step rev] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step sorted\n\x1b[1;30mINFO\x1b[0m [step sorted] start\n\x1b[1;30mINFO\x1b[0m [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\n\x1b[1;30mINFO\x1b[0m [job sorted] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job sorted] completed success\n\x1b[1;30mINFO\x1b[0m [step sorted] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\', job_order=[\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}, \'reverse_sort\': True}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b9792322151224743947536605dc9cca24e185d8 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 0b54605194d27895bfbccb163d89b64dba40161d9771e915b204ef89c0501446 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 924e606ff3341e4daea625839633159c1a0c71d12d64532f78160aa03284c5537f3726613c5fa3ec938e0cb3972113e20f4fde6617c88cc98f7e6ec6001e31b5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n },\n "reverse_sort": true\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step rev\nDEBUG cwltool:workflow_job.py:727 [step rev] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step rev] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step rev] start\nDEBUG cwltool:command_line_tool.py:982 [job rev] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/revtool.cwl as part of step rev\nDEBUG cwltool:command_line_tool.py:988 [job rev] {\n "revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job rev] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job rev] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "revtool_input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "dirname": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job rev] initial work dir {}\nINFO cwltool:job.py:266 [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:job.py:905 [job rev] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 97fe1b50b4582cebc7d853796ebd62e3e163aa3f data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nINFO cwltool:job.py:419 [job rev] completed success\nDEBUG cwltool:job.py:422 [job rev] outputs {\n "revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step rev] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:572 [step rev] completed success\nDEBUG cwltool:job.py:446 [job rev] Removing input staging directory /private/tmp/docker_tmp0onaxo3l\nDEBUG cwltool:job.py:454 [job rev] Removing temporary directory /private/tmp/docker_tmpwl097n7z\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step sorted\nDEBUG cwltool:workflow_job.py:727 [step sorted] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step sorted] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:75 [step sorted] start\nDEBUG cwltool:command_line_tool.py:982 [job sorted] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sorttool.cwl as part of step sorted\nDEBUG cwltool:command_line_tool.py:988 [job sorted] {\n "reverse": true,\n "sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job sorted] path mappings is {\n "file:///private/tmp/docker_tmpo8j3qsh0/output.txt": [\n "/private/tmp/docker_tmpo8j3qsh0/output.txt",\n "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job sorted] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sort"\n },\n {\n "position": [\n 1,\n "reverse"\n ],\n "prefix": "--reverse",\n "datum": true\n },\n {\n "position": [\n 2,\n "sorted_input"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1",\n "path": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "dirname": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job sorted] initial work dir {}\nINFO cwltool:job.py:266 [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\nINFO cwltool:job.py:905 [job sorted] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: b9214658cc453331b62c2282b772a5c063dbd284 data/b9/b9214658cc453331b62c2282b772a5c063dbd284\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nINFO cwltool:job.py:419 [job sorted] completed success\nDEBUG cwltool:job.py:422 [job sorted] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step sorted] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step sorted] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:job.py:446 [job sorted] Removing input staging directory /private/tmp/docker_tmpt9i2u3d_\nDEBUG cwltool:job.py:454 [job sorted] Removing temporary directory /private/tmp/docker_tmp7ypgmrbr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplkmwaaf_/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplkmwaaf_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp46e4pq4y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo8j3qsh0\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: df915edbd6b5e75857277eb6c8e1377f0d051ef1 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4e56225fad8da955eebc34f2c094def00b9a7b6b39c500bd4ba036618c22e6f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 42a067ea2914371f209f8c25161dee0d1589e739c64f3275519f23d0af480afc636ea8b3298663632e89b2033c18a855ad9eb5290298ed00837688a946ac1523 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 553157706bf95e14c524a396a623d0f3f87f8ecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c6eccb1bc96bd4f55d03be6f4c0262a736dd8296ecae60d0d403bc9bfc8ca92b metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: f8c2586c8f0749fe5ef9e772f752c63acc2ba9dc8176e2cd8da9e677b952f7ba5a8410f062937ee19a3db25b2a414ef3566294dec7e6b6d011f21d176f3e4e3f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: ca44d2cee82bdf4159a998516a8b7d97de4becde metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 9abbc3a964398906a0a6c446f05be412b4f818c5df80213eefb95585644407f9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4dd04bc545f060056ec3c0eb38c22e70e30c30f4b3d633c60a802e4fcb4607737e7938f57b1eaea5a7044b23bf39461a15ccd68a344564b0a257cb7c966d8562 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b52bb0536caa8678dee76e093bab66c9f6ab72d8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fe046d6822ede74b785f00faa9e38aeeb92d573926c5e8f0dc3e87ddcf655336 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 3fe06b96dca53c5afed7eee93e58b27dd8330c34ce5436271af797259e4ffbc9790bb32f8cdab7244e1a83d0f8f1137464dc0dd757d841ac69412932cf09a9f9 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e58bcf95cb06e3d42132d9c488c389eb62de0170 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 27f34aff0b66f02249b46599489c42e37efc5de28e05274bba403a11a31bd86e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4f70440a6e4c80363471248e4d36d4df1a61f6bdeebdc41391bab98dcc5715361142776d4dd4dcc2b9f81d4687b83ea3a259c4a52374d0e6bed988bb6cfc8683 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: bb4d8f1c88da465df4d205fe71778cf5ee0c971e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 45e8790efb18825deb4c136d97032976f831b167076b31e43bd6ae66fc7466d7 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: bad9c61094a072702da2befe78c06dc406039eba8d4f5abeb39fb0646589428829d6e32ce91b705be4d0b9eba94cad5ca02e0665a23e9190438ef61b05611244 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'sorted_output\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 0536da382206c737b78578fb4cd56d470854cb65 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: ca8f0addfb91188dc24d6f6f2455b58ba794fa05417a99e239993ca8a25627c4 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 1ecd7b38f4685c4c7c7a124deaf30613ef849999f7aa5afb3b537d294a9e66933052c4e35fcb2d7a37e565e33a918c497349b9fc901cf828c5f9cd592dce1114 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: eac590a030efa84e4abe5c70bfbbe059d59cb909 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c85344af5e84a113da5636b4c42935c478fe1b587b2f84f82aa07465a71ce1d1 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fc05d8795084ee56e93edfd135c625c462e71dfaed99a7dc613264eb2b8a75a518580a187fb580fa9309c4cb1398a6501040c6251a221f31cbe67c5576a5d799 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: a7199d53b1f707ab9bfa7a88f832a843a05da1b5 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 44dad89d06c949f171fb43e2c2a870f92520a7d288460cafadfd19afefb7697c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fed9bf631358efdec9cb96154215b41a76dc6b7cd38eeb794f6a94212e5fcf868dcc776b0cec9d950de8370d3e4399a7c36833da2d5bdebfb0e193d813047ad4 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 825bbdb1ae0c5b4dab6115409f478fd2b7546ef1 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 65c5c5444143e944a90a7ec7fed5e89f3b4195f53a84f0747bca4875ad8602ec bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 9212abe820053e53692266203ba3819ceae75bb7f5d82f74281d7d1e9e0682ee506d9b210ef2d2bae5396e8d0f751bafbdf1f361747bf3cdc4d9aaa247919f25 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance')] - duration: 0.0007942510001157643 - start: 1685951458.580619 - stop: 1685951458.581415 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_revsort_workflow - location: ('tests/test_provenance.py', 74, 'test_revsort_workflow') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - nodeid: tests/test_provenance.py::test_revsort_workflow - when: runtest - location: None - finish pytest_warning_recorded --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut - location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut - location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') - keywords: {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0014417179991141893 - start: 1685951458.583897 - stop: 1685951458.5853388 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - pytest_assertrepr_compare [hook] - config: <_pytest.config.Config object at 0x1043f7730> - op: == - left: 1 - right: 0 - finish pytest_assertrepr_compare --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: > - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut - location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') - keywords: {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: failed - longrepr: {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 46, 'message': "AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))\nassert 1 == 0"}, 'reprtraceback': {'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_revsort_workflow_shortcut(tmp_path: Path) -> None:', ' """Confirm that using \'cwl:tool\' shortcut still snapshots the CWL files."""', '> folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/revsort-job-shortcut.json"),', ' )'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 89, 'message': ''}, 'style': 'long'}}, {'type': 'ReprEntry', 'data': {'lines': [' def cwltool(tmp_path: Path, *args: Any) -> Path:', ' prov_folder = tmp_path / "provenance"', ' prov_folder.mkdir()', ' new_args = ["--provenance", str(prov_folder)]', ' new_args.extend(args)', ' # Run within a temporary directory to not pollute git checkout', ' tmp_dir = tmp_path / "cwltool-run"', ' tmp_dir.mkdir()', ' with working_directory(tmp_dir):', ' status = main(new_args)', '> assert status == 0, f"Failed: cwltool.main({args})"', "E AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))", 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')"), ('args', "('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',)"), ('prov_folder', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')"), ('new_args', "['--provenance', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance', '/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json']"), ('tmp_dir', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 46, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, 'sections': [], 'chain': [({'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_revsort_workflow_shortcut(tmp_path: Path) -> None:', ' """Confirm that using \'cwl:tool\' shortcut still snapshots the CWL files."""', '> folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/revsort-job-shortcut.json"),', ' )'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 89, 'message': ''}, 'style': 'long'}}, {'type': 'ReprEntry', 'data': {'lines': [' def cwltool(tmp_path: Path, *args: Any) -> Path:', ' prov_folder = tmp_path / "provenance"', ' prov_folder.mkdir()', ' new_args = ["--provenance", str(prov_folder)]', ' new_args.extend(args)', ' # Run within a temporary directory to not pollute git checkout', ' tmp_dir = tmp_path / "cwltool-run"', ' tmp_dir.mkdir()', ' with working_directory(tmp_dir):', ' status = main(new_args)', '> assert status == 0, f"Failed: cwltool.main({args})"', "E AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))", 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')"), ('args', "('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',)"), ('prov_folder', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')"), ('new_args', "['--provenance', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance', '/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json']"), ('tmp_dir', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 46, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 46, 'message': "AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))\nassert 1 == 0"}, None)]} - when: call - user_properties: [] - sections: [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mERROR\x1b[0m \x1b[31mGot workflow error\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json",\n "reverse_sort": true,\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "@id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'reverse_sort\': True, \'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 5e5a492f53d25bdd4e5e7e3ee61407036d74c263 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 8322e8a8c8231f681484b7cf2caae8110994310a49cbb0679a9dc40993bd863d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 57b1439b4885ea2220eb4b4177e0c82d5724d29dd75ce4ce5b4041c9a9c705cadc478ed732165222d7fff8788ef51dc4c5478ae1586d34fa3bec637b183cdcd6 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nERROR cwltool:executors.py:250 Got workflow error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: d4e780eac6b995170c5544138e51cee42bf82b02 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 71854d40af17ddaad25710ff92bed3033edc5312cea32640d1780241b99df51f metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: ba634748b2a242590fe4f2f293ea32ab4cae028fc7ba9a83b3ce2964374030766b9b71e13fe231a9e27877e79b5c939c949ce2cab6806a002f4ef8005ea34504 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: fa166224b2884b8c1a7019701241269f0fe8f4ba metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: b220ef2e9661453dc089f3645d905eb38ede5f81267288875ebaa393f440a3b6 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 67dc40c370f4eb425ad35887933493d90057b10fb0d6c65a7b9dd47fd482ce515036fe98304f7a6254891a4240f1f515e792dd7c3610f9d4e38c5954de185854 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 7b845a04531a0aea8b66445b3cb5dfd3cc38987e bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 674fc7391ca2a9c892cc4a7b8f6d69ef84f4debea78506708c389a4611090a94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 350e30ea50137627007116ea6a7b9e3f71a7b9e01835e5e0b82201f45bd7f577cc3f294c98401c2afabc72bd7c331d4a7ad8cb70dcac056749b3d897311a5e03 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')] - duration: 0.9283330289999867 - start: 1685951458.585697 - stop: 1685951459.514008 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_exception_interact [hook] - node: - call: > - report: - finish pytest_exception_interact --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut - location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') - keywords: {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mERROR\x1b[0m \x1b[31mGot workflow error\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json",\n "reverse_sort": true,\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "@id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'reverse_sort\': True, \'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 5e5a492f53d25bdd4e5e7e3ee61407036d74c263 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 8322e8a8c8231f681484b7cf2caae8110994310a49cbb0679a9dc40993bd863d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 57b1439b4885ea2220eb4b4177e0c82d5724d29dd75ce4ce5b4041c9a9c705cadc478ed732165222d7fff8788ef51dc4c5478ae1586d34fa3bec637b183cdcd6 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nERROR cwltool:executors.py:250 Got workflow error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: d4e780eac6b995170c5544138e51cee42bf82b02 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 71854d40af17ddaad25710ff92bed3033edc5312cea32640d1780241b99df51f metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: ba634748b2a242590fe4f2f293ea32ab4cae028fc7ba9a83b3ce2964374030766b9b71e13fe231a9e27877e79b5c939c949ce2cab6806a002f4ef8005ea34504 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: fa166224b2884b8c1a7019701241269f0fe8f4ba metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: b220ef2e9661453dc089f3645d905eb38ede5f81267288875ebaa393f440a3b6 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 67dc40c370f4eb425ad35887933493d90057b10fb0d6c65a7b9dd47fd482ce515036fe98304f7a6254891a4240f1f515e792dd7c3610f9d4e38c5954de185854 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 7b845a04531a0aea8b66445b3cb5dfd3cc38987e bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 674fc7391ca2a9c892cc4a7b8f6d69ef84f4debea78506708c389a4611090a94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 350e30ea50137627007116ea6a7b9e3f71a7b9e01835e5e0b82201f45bd7f577cc3f294c98401c2afabc72bd7c331d4a7ad8cb70dcac056749b3d897311a5e03 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')] - duration: 0.0016798560000097496 - start: 1685951459.699641 - stop: 1685951459.701323 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut - location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_nested_workflow - location: ('tests/test_provenance.py', 98, 'test_nested_workflow') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_nested_workflow - location: ('tests/test_provenance.py', 98, 'test_nested_workflow') - keywords: {'test_nested_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0018565800000942545 - start: 1685951459.703209 - stop: 1685951459.705068 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_nested_workflow - location: ('tests/test_provenance.py', 98, 'test_nested_workflow') - keywords: {'test_nested_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{\n "classout": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class",\n "basename": "Hello.class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _18] start\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step create-tar\n\x1b[1;30mINFO\x1b[0m [step create-tar] start\n\x1b[1;30mINFO\x1b[0m [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nMon Jun 5 09:51:00 CEST 2023\nMon Jun 5 09:51:00 CEST 2023\n\x1b[1;30mINFO\x1b[0m [job create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [step create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step compile\n\x1b[1;30mINFO\x1b[0m [step compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step untar\n\x1b[1;30mINFO\x1b[0m [step untar] start\n\x1b[1;30mINFO\x1b[0m [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\n\x1b[1;30mINFO\x1b[0m [job untar] completed success\n\x1b[1;30mINFO\x1b[0m [step untar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step argument\n\x1b[1;30mINFO\x1b[0m [step argument] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/openjdk:9.0.1-11-slim']\n9.0.1-11-slim: Pulling from library/openjdk\nDigest: sha256:dc239c9a17aa509d4e79dc4980e40a5f0c8af78a9bcefab2b5eedf819f702298\nStatus: Image is up to date for openjdk:9.0.1-11-slim\ndocker.io/library/openjdk:9.0.1-11-slim\n\x1b[1;30mINFO\x1b[0m [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\n\x1b[1;30mINFO\x1b[0m [job argument] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job argument] completed success\n\x1b[1;30mINFO\x1b[0m [step argument] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] completed success\n\x1b[1;30mINFO\x1b[0m [step compile] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 74ece951469a5306ac6512cff2a9f3b25b91c858 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: a0f6fb34d0ba97018b294486569ded02bb6e6e659d3e06c5de4f214582691f36 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: f0dca2f20d6e9cd7b5ca6e9ea53e3c5548164e2b77ca0b2a1f3e785ce12f314ca29d1943f80ee974373ab7ead0031aee08c07bb511c34c82cc951e3bef28c9b0 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _18] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile not ready\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step create-tar\nDEBUG cwltool:workflow_job.py:727 [step create-tar] job input {}\nDEBUG cwltool:workflow_job.py:732 [step create-tar] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step create-tar] start\nDEBUG cwltool:command_line_tool.py:982 [job create-tar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/fbd87079-fe0c-4de9-b99f-0c79323cf2c1 as part of step create-tar\nDEBUG cwltool:command_line_tool.py:988 [job create-tar] {}\nDEBUG cwltool:command_line_tool.py:1000 [job create-tar] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job create-tar] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "date\\ntar cf hello.tar Hello.java\\ndate\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job create-tar] initial work dir {\n "_:5de9498b-d23e-4bbf-b5e6-3d9459eedb80": [\n "public class Hello {\\n public static void main(String[] argv) {\\n System.out.println(\\"Hello from Java\\");\\n }\\n}\\n",\n "/private/tmp/docker_tmpkyipo8y7/Hello.java",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 4864f67aab6874db8b656c7b15bd7cfc595e9571 data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nINFO cwltool:job.py:419 [job create-tar] completed success\nDEBUG cwltool:job.py:422 [job create-tar] outputs {\n "tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step create-tar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:572 [step create-tar] completed success\nDEBUG cwltool:job.py:446 [job create-tar] Removing input staging directory /private/tmp/docker_tmpzx57hfi5\nDEBUG cwltool:job.py:454 [job create-tar] Removing temporary directory /private/tmp/docker_tmp4rtd4n2g\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step compile\nDEBUG cwltool:workflow_job.py:727 [step compile] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step compile] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step compile] start\nDEBUG cwltool:workflow_job.py:498 [workflow compile] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow compile] start\nDEBUG cwltool:workflow_job.py:777 [workflow compile] inputs {\n "ex": "Hello.java",\n "inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:610 [workflow compile] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument not ready\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step untar\nDEBUG cwltool:workflow_job.py:727 [step untar] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step untar] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step untar] start\nDEBUG cwltool:command_line_tool.py:982 [job untar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/tar-param.cwl as part of step untar\nDEBUG cwltool:command_line_tool.py:988 [job untar] {\n "extractfile": "Hello.java",\n "tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job untar] path mappings is {\n "file:///private/tmp/docker_tmpkyipo8y7/hello.tar": [\n "/private/tmp/docker_tmpkyipo8y7/hello.tar",\n "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job untar] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "tar"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "xf"\n },\n {\n "position": [\n 1,\n "tarfile"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9",\n "path": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "dirname": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134"\n }\n },\n {\n "position": [\n 2,\n "extractfile"\n ],\n "datum": "Hello.java"\n }\n]\nDEBUG cwltool:job.py:215 [job untar] initial work dir {}\nINFO cwltool:job.py:266 [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 93035905e94e150874f5a881d39f3c5c6378dd38 data/93/93035905e94e150874f5a881d39f3c5c6378dd38\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nINFO cwltool:job.py:419 [job untar] completed success\nDEBUG cwltool:job.py:422 [job untar] outputs {\n "example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step untar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step untar] completed success\nDEBUG cwltool:job.py:446 [job untar] Removing input staging directory /private/tmp/docker_tmp8uve11w8\nDEBUG cwltool:job.py:454 [job untar] Removing temporary directory /private/tmp/docker_tmpnpvtosz9\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step argument\nDEBUG cwltool:workflow_job.py:727 [step argument] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step argument] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:75 [step argument] start\nDEBUG cwltool:command_line_tool.py:982 [job argument] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/arguments.cwl as part of step argument\nDEBUG cwltool:command_line_tool.py:988 [job argument] {\n "src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job argument] path mappings is {\n "file:///private/tmp/docker_tmpc_ieg46p/Hello.java": [\n "/private/tmp/docker_tmpc_ieg46p/Hello.java",\n "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job argument] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "javac"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-d"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(runtime.outdir)"\n },\n {\n "position": [\n 1,\n "src"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5",\n "path": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "dirname": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/openjdk:9.0.1-11-slim\']\nDEBUG cwltool:job.py:215 [job argument] initial work dir {}\nINFO cwltool:job.py:266 [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\nINFO cwltool:job.py:905 [job argument] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 39e3219327347c05aa3e82236f83aa6d77fe6bfd data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nINFO cwltool:job.py:419 [job argument] completed success\nDEBUG cwltool:job.py:422 [job argument] outputs {\n "classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step argument] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step argument] completed success\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 83049fca7761d12fb0a5da48da3c037c5304a0fc metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 60258aab9b1b640774e4705795ed3f7ae538c98238f3fae97911d4b93bbfaa2d metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 33139ea057934520ce5f2525af14fafb879322770000acdb150ee5aa445568f3588850a5f5951dce7a03937af0e4ae1ecddafaff17b8299b4e9b2d2372aa07e7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0304d4e8c149fbe870496f20f4c073b6946f7fe7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 13120ba16180324a0c690989fede01b2424adce87145cd0da6492b177f8f814c metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 86e81f57bbb1e5335d9dd2921076dfeba39e953bc4214261e7d818a3a7f38ebb9c4367320cf6fa2714c96e00132009d102c6b6604f36fefc1639cdb722d70715 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: cff4ad2216ea628f4975c69699c8e3fc0c3e4632 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 5d742295d8aba73c67424e366c394e0a34f773985c1645c9b6910e35e353afc9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c6b20c2741a3fa0edeb70054d7f72885b90dd62331b41d5f9fb9f2032495d78b83428995111a6ba52d098f57d976c760321811e6ea182d2e2f562976ba5ad1c9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 1fdf97a3b214d0a050db07a554ecfe44b056e655 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 325d75d9f711a5a12feee43188da250d5fdc200b6ca2e33214209fed193a87c8 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8cac58c921bd6a7115ef1dace866bdb2b84dd948cbed5014ab70eae79abe7b30e8ddeafc033659ddb581ac53550230aa818e3623fc55cebae094df17b7b9cd64 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9f2ad16a37a1df641dfe180c8704e88211c46676 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 939e5a54c9079007e36c852408057047622c11cb1d06b2b64b82636d8a1d6762 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 65707a62469cf55e9dcb8fdfe87bf1af958df3846a5de0a6c4732557af5ad6ddfd07fae87e80e7c4c3cef36d0b3b25b03293a5805ddeecf1d86980a7bff1e885 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9be8dfc973c5248324d388bda772ced2eafc5d09 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 4ad66e5bea19ad398ad45267244c6fb7e950340d509df851edbad2fbb844a504 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 63e5b105c46bef759931359c5994f6cff8029bb8a59911a3458df8d1e4e1b98fb3b6f8689c2096670880e2833bd3ae7e369b8e77ef0c7ae613edb86ff6dd9887 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nINFO cwltool:workflow_job.py:539 [workflow compile] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow compile] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step compile] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step compile] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:job.py:446 [job argument] Removing input staging directory /private/tmp/docker_tmpebe5z0v8\nDEBUG cwltool:job.py:454 [job argument] Removing temporary directory /private/tmp/docker_tmpdff4tkfu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpepzg_f_c/Hello.class to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzrpr1a4o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr_sgrnnb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpepzg_f_c\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkyipo8y7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpc_ieg46p\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 19fbff09cc97d57d7241305ed0cb03212f211ae9 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 410b6c9c1c10cc229c8781ddc5074f25f371cdf9b4e6e053758e98931db2f7eb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 6c75e7c3ef6bf96b917b3961bf1350658fec598fb67d194716c7fa281d09ae834cf81cea64f8636e34b2a8391b8d4391e267b526d90b3460ed50ffa35b615b9f metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 42906be32350038218f034e2418bfa414323fecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 54d1a6a2ea333664645b1ef510288b473b2798d0eba102c7d9f83979acdb30ea metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 59de6004ed6286c5bf4461690f1eea3eecec94be8cf7f186aa9100dd447ed2d3f8e78d8bb9a09b712d6bf0c16f036559fb76f2e57f9c9bf47f5b868d5a5b1698 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 54936279704d89dd038e6bb6207276b94ccf52c7 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48a6d44504c674c65ae71bf0186c051343568e8b1796272af0adf58b39dfc015 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 77323c4d9ca07d91bcb9db9f7090422963c30ec31c9cc7312a2619f60dfb0f8632630019a19f57fd3f2bbe2a354d0328dfb60c482f81141a31ea1b3c118e2466 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 76273be200ec2c229e213509b9bb670478dce7f4 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48244946e314f094d1b6c4b6e30a3358b5cbca006e442806c064eb0ffb961c1a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 64a2901aa5304fa5d65408f3a61b12c9131f251d89f4e688f9c3c3cdcba700f7fc67069606af5b24e6196f60e2553a53f51fda4ff970d89a7d91881ff5ffc4b5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: d80b34fd80aa3f9137314feb7021908e2b52cb91 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cc95cb90e86609a55c17cd318a3e5bd9892687cc6df9ba66fc8479dfd0d95aef metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 697c8c7b70137288a5672502d3786e77f04ce6f28f5a549ac71edb9f8bac64d7cb6ee4ef13ce84d9184f865db3ccaa66cf20bc62f31824e4b558a9bb959d6ef4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: f8b1b468869ac1a80043e092868c2277f1d15c64 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1805212079569e9a572fab9cdb3b73665e98e5ca3ec88d9b637ee30ffd026e11 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 036d8f071535a67857917407770951d720c444f3b9057b0bd8194be89066977bcc223f1ad268b552ea07d143c886679c4cbb66d79a0dea214672d54ec41358ff metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'classout\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello.class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 419\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a77f1bf715803e410ab8646eec4bee4f620aca8f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 023017d52b11f799321c82c33eb3f4b053ed57872618d37d30b69ec0c64902f8 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8e911b78c78b0a5146fc24f8adbdf1f253a2d78f6239c81533b0166ebd4f7ed7dd64e7fb3f86a7f62eb6d4288ade648629ef6c28ad1ab4accadc2800a8038123 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 724b068a51d129c5492f28865b3bed0eb22a8dec snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 0727286ce68bebcae06f0cb1da28a58382c9db14f0e4eae7e29f5644483d16cb snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c116c653cd68a7fd934d7df77d24a4977efa1c6505d6c32b138aec44130d40228f7d69bf3b11fb9473e421755e7d592f15b1aa93c988b1ec3249dc84139b7960 snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 7b997f5397fd668969634a4e8c113cec0fbbc5e8 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cdd580b6c0f37c60cc39ef4968184235ade6ab7369329b363c5db7f101f6d3a4 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 3c72796915141289f4e94ec0b83fa5fbd0203d8afb69adf0dcd866a616ddc9a432d071e75e54f3eafcd3d850411b6cfb54643cf123fb246206f49885a0b5fdbf snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b9b609b8713bd5ebed4e83e8074f84648a5f6708 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 6ddc89e25e65a9a6e80de48be06442cef0128b9f1c82ec8d50019223c5bfd866 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 58e44c861533f86faee277fc618bd869781ec5c1203bad37d150dd5efaed44d51198c9fed40ddd62b9ef348e2a9b9f5004d86c9983ee22ac61070b0c588a8229 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a11e6ae3b6824babd50ca5a96395030d203565f6 snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ba73050af0d17a6a24d82aeb88b54150e38189056007f1dd094a59562f30475d snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 57fe970c776bf2b8f283783b6565d886acd7f5974ec7a7a9de547201585a93130c40b494e29bb2a489123dc5d0c30f791c585f1f29dc11ff8d381b16c7d9e348 snapshot/tar-param.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0dd82b60f74970af2204ec209f5d9ba9bcf90ab1 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1991adaba7d0cdd01efb884f896e70162a678d6c019c8af40a628e3e81c958dd metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c8b1f27a515fda5fffc55d93abf31ae91d00fe9077046e16109522c83fd5740e4df390bb7dce1e8d7c5ee00e3d1532e298ee248addec8623f2d88f1f0b5d94d4 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b201b1900b531a5cac833222efcf2ea148ee8e4f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: be90e3007275188cbc913e1d8e0b2901a70917ecb0c4d82a9967a894ad18fc33 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca20cd4c002dea5a664c54c7a7d874ed07461ed50baf0016e4e9c45fdaa16132772748146c0f39bf409004e80e3c2ee9db16490543e86a8e41e45cea5758d3af metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 8e62f08782410be5f7a325ad891118c1c8b048c9 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: af35cf1992cf37219396ab2b24f2c0bc89e1e9d3fa27c63d3f8c8a2a64c2b62a bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c3bdb2ec78cc257d15b637073d81804b259e9bd197b9b0aa71d9a3b66b7eee0df29dbd0f6146ebdb9fee6e3adc073a09a3cd260708cc7890a982c547bb28d165 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance')] - duration: 5.002003371999308 - start: 1685951459.705703 - stop: 1685951464.707586 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_nested_workflow - location: ('tests/test_provenance.py', 98, 'test_nested_workflow') - keywords: {'test_nested_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "classout": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class",\n "basename": "Hello.class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _18] start\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step create-tar\n\x1b[1;30mINFO\x1b[0m [step create-tar] start\n\x1b[1;30mINFO\x1b[0m [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nMon Jun 5 09:51:00 CEST 2023\nMon Jun 5 09:51:00 CEST 2023\n\x1b[1;30mINFO\x1b[0m [job create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [step create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step compile\n\x1b[1;30mINFO\x1b[0m [step compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step untar\n\x1b[1;30mINFO\x1b[0m [step untar] start\n\x1b[1;30mINFO\x1b[0m [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\n\x1b[1;30mINFO\x1b[0m [job untar] completed success\n\x1b[1;30mINFO\x1b[0m [step untar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step argument\n\x1b[1;30mINFO\x1b[0m [step argument] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/openjdk:9.0.1-11-slim']\n9.0.1-11-slim: Pulling from library/openjdk\nDigest: sha256:dc239c9a17aa509d4e79dc4980e40a5f0c8af78a9bcefab2b5eedf819f702298\nStatus: Image is up to date for openjdk:9.0.1-11-slim\ndocker.io/library/openjdk:9.0.1-11-slim\n\x1b[1;30mINFO\x1b[0m [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\n\x1b[1;30mINFO\x1b[0m [job argument] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job argument] completed success\n\x1b[1;30mINFO\x1b[0m [step argument] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] completed success\n\x1b[1;30mINFO\x1b[0m [step compile] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 74ece951469a5306ac6512cff2a9f3b25b91c858 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: a0f6fb34d0ba97018b294486569ded02bb6e6e659d3e06c5de4f214582691f36 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: f0dca2f20d6e9cd7b5ca6e9ea53e3c5548164e2b77ca0b2a1f3e785ce12f314ca29d1943f80ee974373ab7ead0031aee08c07bb511c34c82cc951e3bef28c9b0 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _18] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile not ready\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step create-tar\nDEBUG cwltool:workflow_job.py:727 [step create-tar] job input {}\nDEBUG cwltool:workflow_job.py:732 [step create-tar] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step create-tar] start\nDEBUG cwltool:command_line_tool.py:982 [job create-tar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/fbd87079-fe0c-4de9-b99f-0c79323cf2c1 as part of step create-tar\nDEBUG cwltool:command_line_tool.py:988 [job create-tar] {}\nDEBUG cwltool:command_line_tool.py:1000 [job create-tar] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job create-tar] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "date\\ntar cf hello.tar Hello.java\\ndate\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job create-tar] initial work dir {\n "_:5de9498b-d23e-4bbf-b5e6-3d9459eedb80": [\n "public class Hello {\\n public static void main(String[] argv) {\\n System.out.println(\\"Hello from Java\\");\\n }\\n}\\n",\n "/private/tmp/docker_tmpkyipo8y7/Hello.java",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 4864f67aab6874db8b656c7b15bd7cfc595e9571 data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nINFO cwltool:job.py:419 [job create-tar] completed success\nDEBUG cwltool:job.py:422 [job create-tar] outputs {\n "tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step create-tar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:572 [step create-tar] completed success\nDEBUG cwltool:job.py:446 [job create-tar] Removing input staging directory /private/tmp/docker_tmpzx57hfi5\nDEBUG cwltool:job.py:454 [job create-tar] Removing temporary directory /private/tmp/docker_tmp4rtd4n2g\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step compile\nDEBUG cwltool:workflow_job.py:727 [step compile] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step compile] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step compile] start\nDEBUG cwltool:workflow_job.py:498 [workflow compile] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow compile] start\nDEBUG cwltool:workflow_job.py:777 [workflow compile] inputs {\n "ex": "Hello.java",\n "inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:610 [workflow compile] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument not ready\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step untar\nDEBUG cwltool:workflow_job.py:727 [step untar] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step untar] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step untar] start\nDEBUG cwltool:command_line_tool.py:982 [job untar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/tar-param.cwl as part of step untar\nDEBUG cwltool:command_line_tool.py:988 [job untar] {\n "extractfile": "Hello.java",\n "tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job untar] path mappings is {\n "file:///private/tmp/docker_tmpkyipo8y7/hello.tar": [\n "/private/tmp/docker_tmpkyipo8y7/hello.tar",\n "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job untar] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "tar"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "xf"\n },\n {\n "position": [\n 1,\n "tarfile"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9",\n "path": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "dirname": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134"\n }\n },\n {\n "position": [\n 2,\n "extractfile"\n ],\n "datum": "Hello.java"\n }\n]\nDEBUG cwltool:job.py:215 [job untar] initial work dir {}\nINFO cwltool:job.py:266 [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 93035905e94e150874f5a881d39f3c5c6378dd38 data/93/93035905e94e150874f5a881d39f3c5c6378dd38\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nINFO cwltool:job.py:419 [job untar] completed success\nDEBUG cwltool:job.py:422 [job untar] outputs {\n "example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step untar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step untar] completed success\nDEBUG cwltool:job.py:446 [job untar] Removing input staging directory /private/tmp/docker_tmp8uve11w8\nDEBUG cwltool:job.py:454 [job untar] Removing temporary directory /private/tmp/docker_tmpnpvtosz9\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step argument\nDEBUG cwltool:workflow_job.py:727 [step argument] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step argument] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:75 [step argument] start\nDEBUG cwltool:command_line_tool.py:982 [job argument] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/arguments.cwl as part of step argument\nDEBUG cwltool:command_line_tool.py:988 [job argument] {\n "src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job argument] path mappings is {\n "file:///private/tmp/docker_tmpc_ieg46p/Hello.java": [\n "/private/tmp/docker_tmpc_ieg46p/Hello.java",\n "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job argument] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "javac"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-d"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(runtime.outdir)"\n },\n {\n "position": [\n 1,\n "src"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5",\n "path": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "dirname": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/openjdk:9.0.1-11-slim\']\nDEBUG cwltool:job.py:215 [job argument] initial work dir {}\nINFO cwltool:job.py:266 [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\nINFO cwltool:job.py:905 [job argument] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 39e3219327347c05aa3e82236f83aa6d77fe6bfd data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nINFO cwltool:job.py:419 [job argument] completed success\nDEBUG cwltool:job.py:422 [job argument] outputs {\n "classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step argument] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step argument] completed success\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 83049fca7761d12fb0a5da48da3c037c5304a0fc metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 60258aab9b1b640774e4705795ed3f7ae538c98238f3fae97911d4b93bbfaa2d metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 33139ea057934520ce5f2525af14fafb879322770000acdb150ee5aa445568f3588850a5f5951dce7a03937af0e4ae1ecddafaff17b8299b4e9b2d2372aa07e7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0304d4e8c149fbe870496f20f4c073b6946f7fe7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 13120ba16180324a0c690989fede01b2424adce87145cd0da6492b177f8f814c metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 86e81f57bbb1e5335d9dd2921076dfeba39e953bc4214261e7d818a3a7f38ebb9c4367320cf6fa2714c96e00132009d102c6b6604f36fefc1639cdb722d70715 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: cff4ad2216ea628f4975c69699c8e3fc0c3e4632 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 5d742295d8aba73c67424e366c394e0a34f773985c1645c9b6910e35e353afc9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c6b20c2741a3fa0edeb70054d7f72885b90dd62331b41d5f9fb9f2032495d78b83428995111a6ba52d098f57d976c760321811e6ea182d2e2f562976ba5ad1c9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 1fdf97a3b214d0a050db07a554ecfe44b056e655 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 325d75d9f711a5a12feee43188da250d5fdc200b6ca2e33214209fed193a87c8 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8cac58c921bd6a7115ef1dace866bdb2b84dd948cbed5014ab70eae79abe7b30e8ddeafc033659ddb581ac53550230aa818e3623fc55cebae094df17b7b9cd64 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9f2ad16a37a1df641dfe180c8704e88211c46676 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 939e5a54c9079007e36c852408057047622c11cb1d06b2b64b82636d8a1d6762 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 65707a62469cf55e9dcb8fdfe87bf1af958df3846a5de0a6c4732557af5ad6ddfd07fae87e80e7c4c3cef36d0b3b25b03293a5805ddeecf1d86980a7bff1e885 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9be8dfc973c5248324d388bda772ced2eafc5d09 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 4ad66e5bea19ad398ad45267244c6fb7e950340d509df851edbad2fbb844a504 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 63e5b105c46bef759931359c5994f6cff8029bb8a59911a3458df8d1e4e1b98fb3b6f8689c2096670880e2833bd3ae7e369b8e77ef0c7ae613edb86ff6dd9887 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nINFO cwltool:workflow_job.py:539 [workflow compile] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow compile] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step compile] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step compile] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:job.py:446 [job argument] Removing input staging directory /private/tmp/docker_tmpebe5z0v8\nDEBUG cwltool:job.py:454 [job argument] Removing temporary directory /private/tmp/docker_tmpdff4tkfu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpepzg_f_c/Hello.class to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzrpr1a4o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr_sgrnnb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpepzg_f_c\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkyipo8y7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpc_ieg46p\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 19fbff09cc97d57d7241305ed0cb03212f211ae9 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 410b6c9c1c10cc229c8781ddc5074f25f371cdf9b4e6e053758e98931db2f7eb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 6c75e7c3ef6bf96b917b3961bf1350658fec598fb67d194716c7fa281d09ae834cf81cea64f8636e34b2a8391b8d4391e267b526d90b3460ed50ffa35b615b9f metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 42906be32350038218f034e2418bfa414323fecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 54d1a6a2ea333664645b1ef510288b473b2798d0eba102c7d9f83979acdb30ea metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 59de6004ed6286c5bf4461690f1eea3eecec94be8cf7f186aa9100dd447ed2d3f8e78d8bb9a09b712d6bf0c16f036559fb76f2e57f9c9bf47f5b868d5a5b1698 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 54936279704d89dd038e6bb6207276b94ccf52c7 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48a6d44504c674c65ae71bf0186c051343568e8b1796272af0adf58b39dfc015 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 77323c4d9ca07d91bcb9db9f7090422963c30ec31c9cc7312a2619f60dfb0f8632630019a19f57fd3f2bbe2a354d0328dfb60c482f81141a31ea1b3c118e2466 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 76273be200ec2c229e213509b9bb670478dce7f4 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48244946e314f094d1b6c4b6e30a3358b5cbca006e442806c064eb0ffb961c1a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 64a2901aa5304fa5d65408f3a61b12c9131f251d89f4e688f9c3c3cdcba700f7fc67069606af5b24e6196f60e2553a53f51fda4ff970d89a7d91881ff5ffc4b5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: d80b34fd80aa3f9137314feb7021908e2b52cb91 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cc95cb90e86609a55c17cd318a3e5bd9892687cc6df9ba66fc8479dfd0d95aef metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 697c8c7b70137288a5672502d3786e77f04ce6f28f5a549ac71edb9f8bac64d7cb6ee4ef13ce84d9184f865db3ccaa66cf20bc62f31824e4b558a9bb959d6ef4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: f8b1b468869ac1a80043e092868c2277f1d15c64 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1805212079569e9a572fab9cdb3b73665e98e5ca3ec88d9b637ee30ffd026e11 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 036d8f071535a67857917407770951d720c444f3b9057b0bd8194be89066977bcc223f1ad268b552ea07d143c886679c4cbb66d79a0dea214672d54ec41358ff metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'classout\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello.class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 419\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a77f1bf715803e410ab8646eec4bee4f620aca8f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 023017d52b11f799321c82c33eb3f4b053ed57872618d37d30b69ec0c64902f8 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8e911b78c78b0a5146fc24f8adbdf1f253a2d78f6239c81533b0166ebd4f7ed7dd64e7fb3f86a7f62eb6d4288ade648629ef6c28ad1ab4accadc2800a8038123 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 724b068a51d129c5492f28865b3bed0eb22a8dec snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 0727286ce68bebcae06f0cb1da28a58382c9db14f0e4eae7e29f5644483d16cb snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c116c653cd68a7fd934d7df77d24a4977efa1c6505d6c32b138aec44130d40228f7d69bf3b11fb9473e421755e7d592f15b1aa93c988b1ec3249dc84139b7960 snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 7b997f5397fd668969634a4e8c113cec0fbbc5e8 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cdd580b6c0f37c60cc39ef4968184235ade6ab7369329b363c5db7f101f6d3a4 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 3c72796915141289f4e94ec0b83fa5fbd0203d8afb69adf0dcd866a616ddc9a432d071e75e54f3eafcd3d850411b6cfb54643cf123fb246206f49885a0b5fdbf snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b9b609b8713bd5ebed4e83e8074f84648a5f6708 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 6ddc89e25e65a9a6e80de48be06442cef0128b9f1c82ec8d50019223c5bfd866 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 58e44c861533f86faee277fc618bd869781ec5c1203bad37d150dd5efaed44d51198c9fed40ddd62b9ef348e2a9b9f5004d86c9983ee22ac61070b0c588a8229 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a11e6ae3b6824babd50ca5a96395030d203565f6 snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ba73050af0d17a6a24d82aeb88b54150e38189056007f1dd094a59562f30475d snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 57fe970c776bf2b8f283783b6565d886acd7f5974ec7a7a9de547201585a93130c40b494e29bb2a489123dc5d0c30f791c585f1f29dc11ff8d381b16c7d9e348 snapshot/tar-param.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0dd82b60f74970af2204ec209f5d9ba9bcf90ab1 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1991adaba7d0cdd01efb884f896e70162a678d6c019c8af40a628e3e81c958dd metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c8b1f27a515fda5fffc55d93abf31ae91d00fe9077046e16109522c83fd5740e4df390bb7dce1e8d7c5ee00e3d1532e298ee248addec8623f2d88f1f0b5d94d4 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b201b1900b531a5cac833222efcf2ea148ee8e4f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: be90e3007275188cbc913e1d8e0b2901a70917ecb0c4d82a9967a894ad18fc33 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca20cd4c002dea5a664c54c7a7d874ed07461ed50baf0016e4e9c45fdaa16132772748146c0f39bf409004e80e3c2ee9db16490543e86a8e41e45cea5758d3af metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 8e62f08782410be5f7a325ad891118c1c8b048c9 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: af35cf1992cf37219396ab2b24f2c0bc89e1e9d3fa27c63d3f8c8a2a64c2b62a bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c3bdb2ec78cc257d15b637073d81804b259e9bd197b9b0aa71d9a3b66b7eee0df29dbd0f6146ebdb9fee6e3adc073a09a3cd260708cc7890a982c547bb28d165 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance')] - duration: 0.00113051800053654 - start: 1685951464.710773 - stop: 1685951464.711905 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_nested_workflow - location: ('tests/test_provenance.py', 98, 'test_nested_workflow') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - nodeid: tests/test_provenance.py::test_nested_workflow - when: runtest - location: None - finish pytest_warning_recorded --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_secondary_files_implicit - location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_secondary_files_implicit - location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') - keywords: {'test_secondary_files_implicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0012492460000430583 - start: 1685951464.7161531 - stop: 1685951464.717403 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - early skip of rewriting module: encodings.ascii [assertion] - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_secondary_files_implicit - location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') - keywords: {'test_secondary_files_implicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'--file1\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7fbe1688c021dd47067816cb1915f194a21b192a workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: fdd353f2fc1a5ce060db48433d4c5d39841c3a16a7b3859ecf40c5d0559585cb workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5af67683ddcf0dc25317f9299432e1b480cba92fefc530bb82144c0b46d090163964253480d1d2b57d8d93bc800be27c6a17552dff8d5d285dfea3792633143a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx",\n "size": 3\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpwlagwb74\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpneari7wr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmprjpz3kex\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm23vbaqp\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b4bef5453619901d1f8f99b5ae6de84b0d9e639b metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 5db39cc34f5ff26b64a03b03b9101fecc2312db65289fe2d1be735727992d8bd metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 8d283d305c0e6d11608b05d9a5e1ba5a75fb4aba75402c34b62e6d7daa1524e3e4995c7b5b7dd09e2e1b461a78c125bc27d82023ed600a5efe3ca285ad10ea97 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 8727ee5875ce1f873aaea8acd610451c6f552485 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 7ea7c1f314778c5b956cac5c77bce95ea6b88611ebbc7066030f869d1db4451d metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: bfc8b1282a1fb06945d4fe7918b05d4f0406bbf7cb97de9e7fc3a34a9d24662816b96a4494d9a1063a86717119f908eb3bf90fe45fe4ef1c346c31b9266615c3 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 137c02dbe6b251a0db3df717988e236021b8999b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 563c5a34f521209ac347f8053149f64041ee7b452c394b4d8c04be39be52d09c metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 2eb1f8f6df902d2db5dab2f042daad6a2b591ba84f6017b4920c49d9a72328f2c0e3b8624a9d3b4740645ab3df6fcbfea29f90b796df9be09a37cf9d455769dc metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: f958ba8327cc8b9af11b209e763c08fd828c4aae metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9eee73bac677248e20e3fdc1b3945afaa24f84f31779a432ecc800f5959ac994 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 98aff7bc546d9f42dfcb7cfc86031061cd09819e93cafb46dea0818f5f55023540eed22292a07e8cbee2e3b5a0a3da1b5096d16a38d308112c5b359c4a7e66ef metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 28ac6c4bb8ee879415c09c5c428f9e146863163b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd2b49ac8dce047e8c28351499fefd31d5acd14bd37d5bbb2a984b091accd35d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5a11c7149e3fe38c8365859626f63e90a4a2edbd1603d17ab341ef329bbe5a0b5408df2f612212175eec6fef219878b2cd631e8924ff2f66fab9df76f87a5d2b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 52e03863abba9f946950a2419bc5a3c9d593fd04 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 8e79daf03e3958103d27e310d0879c8812989df38d007346f55fb9433c4108c8 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 00f022778fd2a8b71a936a2bb5b382645d9663735588b29c3a4228989d43026867c3654b71a7087b9bdd09ebcdf95d5e97d22cabef6d0404bff05a436c15996b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 4b5fce360bf0db096420ddf360cb05fb63abef9a metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 12c59130a589553031e8a732559d20225da263aa19d2b43b4f23f2ff47a13396 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: a0f2b7ecf70b39b1e7b84ddab845455bf81f04019ecf1810b9540809be18cfb5a5fcdeb90986c4b11d0d86c85d38ced387beb5248a97e75460019687346cca41 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7da08c3bcf057f5790aae85a316cc4c7e84e8dae metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9822a8bb8f23ff4a5f546df0e1901dac8ce404c90cc9e864c932e858f342296c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 20961f19fd0db8bf533ce8aa98d561c15d672364183fc007e488c01e40271698363b6d1e35edfd4d109b9863391b666e44cb49cbec572343804ee8aec795de28 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3a83e9297c5eca6e6de723837360f84464d4ee94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 57f04fd3cbd44703b65a45ec0acd6b1e56243dd599476dff375f2c868198939d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 7eca04aa9b2734f1b61e65c7f009cd6ddd45735a0c303dd0653b766f411e9fdea1255c5db384dd0b3f787f5b1920fbacdea475948ad439ac70e2589a09f42b46 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance')] - duration: 1.082738922000317 - start: 1685951464.7178009 - stop: 1685951465.800514 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_secondary_files_implicit - location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') - keywords: {'test_secondary_files_implicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'--file1\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7fbe1688c021dd47067816cb1915f194a21b192a workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: fdd353f2fc1a5ce060db48433d4c5d39841c3a16a7b3859ecf40c5d0559585cb workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5af67683ddcf0dc25317f9299432e1b480cba92fefc530bb82144c0b46d090163964253480d1d2b57d8d93bc800be27c6a17552dff8d5d285dfea3792633143a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx",\n "size": 3\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpwlagwb74\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpneari7wr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmprjpz3kex\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm23vbaqp\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b4bef5453619901d1f8f99b5ae6de84b0d9e639b metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 5db39cc34f5ff26b64a03b03b9101fecc2312db65289fe2d1be735727992d8bd metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 8d283d305c0e6d11608b05d9a5e1ba5a75fb4aba75402c34b62e6d7daa1524e3e4995c7b5b7dd09e2e1b461a78c125bc27d82023ed600a5efe3ca285ad10ea97 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 8727ee5875ce1f873aaea8acd610451c6f552485 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 7ea7c1f314778c5b956cac5c77bce95ea6b88611ebbc7066030f869d1db4451d metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: bfc8b1282a1fb06945d4fe7918b05d4f0406bbf7cb97de9e7fc3a34a9d24662816b96a4494d9a1063a86717119f908eb3bf90fe45fe4ef1c346c31b9266615c3 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 137c02dbe6b251a0db3df717988e236021b8999b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 563c5a34f521209ac347f8053149f64041ee7b452c394b4d8c04be39be52d09c metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 2eb1f8f6df902d2db5dab2f042daad6a2b591ba84f6017b4920c49d9a72328f2c0e3b8624a9d3b4740645ab3df6fcbfea29f90b796df9be09a37cf9d455769dc metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: f958ba8327cc8b9af11b209e763c08fd828c4aae metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9eee73bac677248e20e3fdc1b3945afaa24f84f31779a432ecc800f5959ac994 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 98aff7bc546d9f42dfcb7cfc86031061cd09819e93cafb46dea0818f5f55023540eed22292a07e8cbee2e3b5a0a3da1b5096d16a38d308112c5b359c4a7e66ef metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 28ac6c4bb8ee879415c09c5c428f9e146863163b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd2b49ac8dce047e8c28351499fefd31d5acd14bd37d5bbb2a984b091accd35d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5a11c7149e3fe38c8365859626f63e90a4a2edbd1603d17ab341ef329bbe5a0b5408df2f612212175eec6fef219878b2cd631e8924ff2f66fab9df76f87a5d2b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 52e03863abba9f946950a2419bc5a3c9d593fd04 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 8e79daf03e3958103d27e310d0879c8812989df38d007346f55fb9433c4108c8 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 00f022778fd2a8b71a936a2bb5b382645d9663735588b29c3a4228989d43026867c3654b71a7087b9bdd09ebcdf95d5e97d22cabef6d0404bff05a436c15996b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 4b5fce360bf0db096420ddf360cb05fb63abef9a metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 12c59130a589553031e8a732559d20225da263aa19d2b43b4f23f2ff47a13396 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: a0f2b7ecf70b39b1e7b84ddab845455bf81f04019ecf1810b9540809be18cfb5a5fcdeb90986c4b11d0d86c85d38ced387beb5248a97e75460019687346cca41 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7da08c3bcf057f5790aae85a316cc4c7e84e8dae metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9822a8bb8f23ff4a5f546df0e1901dac8ce404c90cc9e864c932e858f342296c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 20961f19fd0db8bf533ce8aa98d561c15d672364183fc007e488c01e40271698363b6d1e35edfd4d109b9863391b666e44cb49cbec572343804ee8aec795de28 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3a83e9297c5eca6e6de723837360f84464d4ee94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 57f04fd3cbd44703b65a45ec0acd6b1e56243dd599476dff375f2c868198939d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 7eca04aa9b2734f1b61e65c7f009cd6ddd45735a0c303dd0653b766f411e9fdea1255c5db384dd0b3f787f5b1920fbacdea475948ad439ac70e2589a09f42b46 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance')] - duration: 0.0008646879996376811 - start: 1685951465.802495 - stop: 1685951465.803361 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_secondary_files_implicit - location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - nodeid: tests/test_provenance.py::test_secondary_files_implicit - when: runtest - location: None - finish pytest_warning_recorded --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_secondary_files_explicit - location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_secondary_files_explicit - location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') - keywords: {'test_secondary_files_explicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.022172081999997317 - start: 1685951465.808274 - stop: 1685951465.8304498 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_secondary_files_explicit - location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') - keywords: {'test_secondary_files_explicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\n\x1b[1;30mINFO\x1b[0m [workflow _20] start\n\x1b[1;30mINFO\x1b[0m [workflow _20] starting step step1_4\n\x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[1;30mINFO\x1b[0m [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\n\x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _20] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ab5d55af482cae1b1829c3da3ee604ee1fb46e6c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: e16b2b9f3a4ea3c4db3ad2bb71e39cdd02c1fde2a446528a68596c88de6ce0ad workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0173fb349bad74105b30c7b54ebfc79bc650689ee08d2810530ae536a1b064eaf25c7b9f15d9c9dfd3e685437e64a2e8d5c55dd9ac21dae1ac0ee2dc95b3c641 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmp9gj9l2fa\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp46c_retm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5ft4gx95\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp96w7gil\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 509e405f0bd8ef93211df57e39be176d12666adc metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 262ec7432d66db0b5ed1cd59aa1af4cd4be1124dbc4af94e86bb6b512289b670 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0119a8de57eb87221919bb6f241bdbe06282b70055adb1d5ae33b9c6f69d081928b3f227305cef219b208ab543d013f5244e55ec7b86517988eaed08f44786f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 45b1c340c57cf230ed17b4e630abdf1efade240e metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: eb6898093916925d311c393e4d05c7526bb1cc611d0dde25b34dd9e93b53bbc4 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 3bf0f3cd885ac1a11daa3a4ddd0c2a1629c6ca2c4ebbb55721070a7aab577a15e431939a7983d567fdfc52b7c6cd4ac9cc7301dc550254a3f5c54bc614f33337 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 38e4d26d88163d39f1f79746d91c385a30ee9225 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0541fdfe699859ca640f637778cffea97fd5bb4b10fae765cca532bb51594598 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: dd848f7099d65e87f01861744621b13563715b0af772ac3f9c254aaf22da244075483bb03cd153771798371887f6435b579e557f5fc8e0b55abcbd63d11b3671 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0a9161af759436c0940176a0ee92ac46d033a8d2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d975c4b3006cb518b3712877f983b68a2f38e2860b23bbda21d4d5c6bc82482d metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: af800227b8ede5af124ae87add535d60d7565a31b2e0923532a6442d21e755820ef1dee20d54db2aae2585bbdc1f1d566b1a76a4d251b80d6183146da3b14b9c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 6f16628a75ecb5bc263b08aa80b2b04c289f6b85 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d7a309d015efc43f7c0d10319bd7866a9e569b1ceb945c129bfc0108f1baeeb7 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 60585141255cb9b43faafbfa26e49d21ddaeff3718becc211fc229d7b9dc2201ae89245239fc3ff9e03726bd8d99faa864df8eb661810117fb2a43f868188cb3 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0077decebf928c4d8aebf6cd1b9c40ae95443eb6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ccfe9486f117718bb534393411f3535d23abe939688867cd7fb7666948a96040 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 5f7ed9ffdc499c78afe431fa0d3ed7bd2942590ddb4cdb42b728daae7644af1f50f352669a364b61880354e56de96674c7b9faa918f33ebd112dc80f3194aa5a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ecdb0d529e82bcfae2510df67a6c624ec91cb4eb metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: f3498f65cdd7f44b2f46cdc5f8a6630bd922452b6bed63648fd8a0b0636b53e9 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 140511736f43c0e44321a2d677bb2e54684fa8e564d650558381799123517ea7a27402ecf6c826c0651360dbc351f4903847f1dc7552ecbc7bc5f372963395f7 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b73fda4904dd1bea80c96c9fc89e49aabbd83fff metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 9f14d52b82857ac1b7a45eb1bf0f6ee22105533f54c1af788fec3744102e8d97 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: b5c96592dbe7dd23e27053f734d227f91c089e42395a9a812dc4994fce5850b58c7ae04d804f92a0041ed0487a26a4e0011cd626bcd86621ae9cd773d631daae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: a28a0bc657b6e1797cdbfe4343a9adfad7fbc539 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: b32be96d6dc9f72b299be94d867dd45f884d5e0f5c416b98f8f03e691ddecec3 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 6145e7ae857af5949152de4f2773425ea722b736616597d7c4766ad6b85b57435c37240b545b770e500e565af57ba9ae25b498dfaa8c31003b65f066cfb9a62b bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance')] - duration: 1.0753109860006589 - start: 1685951465.8310468 - stop: 1685951466.9063349 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_secondary_files_explicit - location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') - keywords: {'test_secondary_files_explicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\n\x1b[1;30mINFO\x1b[0m [workflow _20] start\n\x1b[1;30mINFO\x1b[0m [workflow _20] starting step step1_4\n\x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[1;30mINFO\x1b[0m [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\n\x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _20] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ab5d55af482cae1b1829c3da3ee604ee1fb46e6c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: e16b2b9f3a4ea3c4db3ad2bb71e39cdd02c1fde2a446528a68596c88de6ce0ad workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0173fb349bad74105b30c7b54ebfc79bc650689ee08d2810530ae536a1b064eaf25c7b9f15d9c9dfd3e685437e64a2e8d5c55dd9ac21dae1ac0ee2dc95b3c641 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmp9gj9l2fa\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp46c_retm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5ft4gx95\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp96w7gil\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 509e405f0bd8ef93211df57e39be176d12666adc metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 262ec7432d66db0b5ed1cd59aa1af4cd4be1124dbc4af94e86bb6b512289b670 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0119a8de57eb87221919bb6f241bdbe06282b70055adb1d5ae33b9c6f69d081928b3f227305cef219b208ab543d013f5244e55ec7b86517988eaed08f44786f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 45b1c340c57cf230ed17b4e630abdf1efade240e metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: eb6898093916925d311c393e4d05c7526bb1cc611d0dde25b34dd9e93b53bbc4 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 3bf0f3cd885ac1a11daa3a4ddd0c2a1629c6ca2c4ebbb55721070a7aab577a15e431939a7983d567fdfc52b7c6cd4ac9cc7301dc550254a3f5c54bc614f33337 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 38e4d26d88163d39f1f79746d91c385a30ee9225 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0541fdfe699859ca640f637778cffea97fd5bb4b10fae765cca532bb51594598 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: dd848f7099d65e87f01861744621b13563715b0af772ac3f9c254aaf22da244075483bb03cd153771798371887f6435b579e557f5fc8e0b55abcbd63d11b3671 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0a9161af759436c0940176a0ee92ac46d033a8d2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d975c4b3006cb518b3712877f983b68a2f38e2860b23bbda21d4d5c6bc82482d metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: af800227b8ede5af124ae87add535d60d7565a31b2e0923532a6442d21e755820ef1dee20d54db2aae2585bbdc1f1d566b1a76a4d251b80d6183146da3b14b9c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 6f16628a75ecb5bc263b08aa80b2b04c289f6b85 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d7a309d015efc43f7c0d10319bd7866a9e569b1ceb945c129bfc0108f1baeeb7 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 60585141255cb9b43faafbfa26e49d21ddaeff3718becc211fc229d7b9dc2201ae89245239fc3ff9e03726bd8d99faa864df8eb661810117fb2a43f868188cb3 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0077decebf928c4d8aebf6cd1b9c40ae95443eb6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ccfe9486f117718bb534393411f3535d23abe939688867cd7fb7666948a96040 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 5f7ed9ffdc499c78afe431fa0d3ed7bd2942590ddb4cdb42b728daae7644af1f50f352669a364b61880354e56de96674c7b9faa918f33ebd112dc80f3194aa5a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ecdb0d529e82bcfae2510df67a6c624ec91cb4eb metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: f3498f65cdd7f44b2f46cdc5f8a6630bd922452b6bed63648fd8a0b0636b53e9 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 140511736f43c0e44321a2d677bb2e54684fa8e564d650558381799123517ea7a27402ecf6c826c0651360dbc351f4903847f1dc7552ecbc7bc5f372963395f7 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b73fda4904dd1bea80c96c9fc89e49aabbd83fff metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 9f14d52b82857ac1b7a45eb1bf0f6ee22105533f54c1af788fec3744102e8d97 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: b5c96592dbe7dd23e27053f734d227f91c089e42395a9a812dc4994fce5850b58c7ae04d804f92a0041ed0487a26a4e0011cd626bcd86621ae9cd773d631daae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: a28a0bc657b6e1797cdbfe4343a9adfad7fbc539 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: b32be96d6dc9f72b299be94d867dd45f884d5e0f5c416b98f8f03e691ddecec3 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 6145e7ae857af5949152de4f2773425ea722b736616597d7c4766ad6b85b57435c37240b545b770e500e565af57ba9ae25b498dfaa8c31003b65f066cfb9a62b bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance')] - duration: 0.0012781379991793074 - start: 1685951466.908513 - stop: 1685951466.9097931 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_secondary_files_explicit - location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - nodeid: tests/test_provenance.py::test_secondary_files_explicit - when: runtest - location: None - finish pytest_warning_recorded --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_dont_require_inputs - location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_dont_require_inputs - location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') - keywords: {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0014646170002379222 - start: 1685951466.91312 - stop: 1685951466.914585 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_dont_require_inputs - location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') - keywords: {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nusage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\n [-h] --input INPUT [job_order]\n/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script: error: the following arguments are required: --input\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 1.982607547999578 - start: 1685951466.914974 - stop: 1685951468.897533 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_dont_require_inputs - location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') - keywords: {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nusage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\n [-h] --input INPUT [job_order]\n/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script: error: the following arguments are required: --input\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.00028186799954710295 - start: 1685951468.898069 - stop: 1685951468.8983521 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_dont_require_inputs - location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: None - pytest_runtest_logstart [hook] - nodeid: tests/test_validate_js.py::test_validate_js_expressions - location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> <_pytest.logging.LogCaptureFixture object at 0x107214a60> [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_validate_js_expressions - location: ('tests/test_validate_js.py', 36, 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pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_validate_js_expressions - location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') - keywords: {'test_validate_js_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:08]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.\x1b[0m\n"), ('Captured log call', "WARNING cwltool:validate_js.py:208 JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.")] - duration: 0.016739755000344303 - start: 1685951468.9009879 - stop: 1685951468.9177291 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: None - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1043f7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_validate_js_expressions - location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') - keywords: {'test_validate_js_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:08]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.\x1b[0m\n"), ('Captured log call', "WARNING cwltool:validate_js.py:208 JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.")] - duration: 0.0022302220004348783 - start: 1685951468.91821 - stop: 1685951468.920442 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_validate_js.py::test_validate_js_expressions - location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - finish pytest_runtestloop --> True [hook] - pytest_sessionfinish [hook] - session: testsfailed=1 testscollected=664> - exitstatus: 1 - finish pytest_sessionfinish --> [] [hook] - pytest_unconfigure [hook] - config: <_pytest.config.Config object at 0x1043f7730> - finish pytest_unconfigure --> [] [hook] - tests/test_tmpdir.py::test_runtimeContext_respects_tmp_outdir_prefix - location: ('tests/test_tmpdir.py', 253, 'test_runtimeContext_respects_tmp_outdir_prefix') - keywords: {'test_runtimeContext_respects_tmp_outdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.0006812609999542474 - start: 1685951464.2931268 - stop: 1685951464.293809 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_tmpdir.py::test_runtimeContext_respects_tmp_outdir_prefix - location: ('tests/test_tmpdir.py', 253, 'test_runtimeContext_respects_tmp_outdir_prefix') - keywords: {'test_runtimeContext_respects_tmp_outdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0003360400005476549 - start: 1685951464.294197 - stop: 1685951464.294534 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_tmpdir.py::test_runtimeContext_respects_tmp_outdir_prefix - location: ('tests/test_tmpdir.py', 253, 'test_runtimeContext_respects_tmp_outdir_prefix') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_tmpdir.py::test_remove_tmpdirs - location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_tmpdir.py::test_remove_tmpdirs - location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') - keywords: {'test_remove_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0015675119993829867 - start: 1685951464.296684 - stop: 1685951464.298253 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_tmpdir.py::test_remove_tmpdirs - location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') - keywords: {'test_remove_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nHello\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello"\n }\n]\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/2yfuzdes\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/a2i94b9v\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.6808559439996316 - start: 1685951464.298953 - stop: 1685951464.979794 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_tmpdir.py::test_remove_tmpdirs - location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') - keywords: {'test_remove_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nHello\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello"\n }\n]\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/2yfuzdes\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/a2i94b9v\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0005884539996259264 - start: 1685951464.980832 - stop: 1685951464.9814222 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_tmpdir.py::test_remove_tmpdirs - location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: ]> - pytest_runtest_logstart [hook] - nodeid: tests/test_tmpdir.py::test_leave_tmpdirs - location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_tmpdir.py::test_leave_tmpdirs - location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') - keywords: {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0016575850004301174 - start: 1685951464.983828 - stop: 1685951464.9854872 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_tmpdir.py::test_leave_tmpdirs - location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') - keywords: {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env4.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env4.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env4.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env4.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env4.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python3"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "env0.py"\n }\n]\nDEBUG cwltool:job.py:215 [job env4.cwl] initial work dir {\n "_:71d3e5f1-6a63-4f12-8e4e-da560d54b9f0": [\n "import os\\nfor k, v in os.environ.items():\\n print(f\\"{k}={v}\\", end=\\"\\\\0\\")\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/env0.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job env4.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj$ python3 \\\n env0.py > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env4.cwl] completed success\nDEBUG cwltool:job.py:422 [job env4.cwl] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b",\n "basename": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameroot": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6da6366e8e172fcac257989bcfedf15da64e9a2a",\n "size": 1261,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/out/062565172eb482b02386f50adec0303a9a80c77b\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.8227042449998407 - start: 1685951464.986022 - stop: 1685951465.8087091 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: ]> - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_tmpdir.py::test_leave_tmpdirs - location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') - keywords: {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env4.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env4.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env4.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env4.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env4.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python3"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "env0.py"\n }\n]\nDEBUG cwltool:job.py:215 [job env4.cwl] initial work dir {\n "_:71d3e5f1-6a63-4f12-8e4e-da560d54b9f0": [\n "import os\\nfor k, v in os.environ.items():\\n print(f\\"{k}={v}\\", end=\\"\\\\0\\")\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/env0.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job env4.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj$ python3 \\\n env0.py > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env4.cwl] completed success\nDEBUG cwltool:job.py:422 [job env4.cwl] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b",\n "basename": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameroot": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6da6366e8e172fcac257989bcfedf15da64e9a2a",\n "size": 1261,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/out/062565172eb482b02386f50adec0303a9a80c77b\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.019946255999457208 - start: 1685951465.809982 - stop: 1685951465.82993 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_tmpdir.py::test_leave_tmpdirs - location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: ]> - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: ]> - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> help with c [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> -#!/usr/bin/env cwl-runner - -cwlVersion: v1.0 -class: ExpressionTool - -inputs: - foo: - type: - type: record - fields: - one: File - two: string - -expression: $(inputs.foo.two) - -outputs: [] - [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - finish pytest_fixture_setup --> at 0x10b9b5cf0> [hook] - pytest_fixture_setup [hook] - fixturedef: - request: ]>> - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: ]' when='setup' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') - keywords: {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0019066180002482724 - start: 1685951465.833351 - stop: 1685951465.835259 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: ]> - pytest_pyfunc_call [hook] - pyfuncitem: ]> - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: ]' when='call' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') - keywords: {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script\n [-h] --foo.one FOO.ONE --foo.two FOO.TWO [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --foo.one FOO.ONE\n --foo.two FOO.TWO\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'")] - duration: 0.6442673579995244 - start: 1685951465.835901 - stop: 1685951466.480154 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: ]> - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: ]>> - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: ]> - call: - finish pytest_runtest_makereport --> ]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: ]' when='teardown' outcome='passed'> - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') - keywords: {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script\n [-h] --foo.one FOO.ONE --foo.two FOO.TWO [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --foo.one FOO.ONE\n --foo.two FOO.TWO\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'")] - duration: 0.00038592599958064966 - start: 1685951466.4809642 - stop: 1685951466.481351 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparser_with_doc - location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparser_with_doc - location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') - keywords: {'test_argparser_with_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0002025419998972211 - start: 1685951466.483218 - stop: 1685951466.4834208 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparser_with_doc - location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') - keywords: {'test_argparser_with_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'")] - duration: 0.011666497999613057 - start: 1685951466.483816 - stop: 1685951466.4954839 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: 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('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> ['--file_paths', '/home/bart/cwl_test/test2'] [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> ['/home/bart/cwl_test/test2'] [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]') - keywords: {'test_argparse_append_with_default[job_order1-expected_values1]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order1-expected_values1': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0005410029998529353 - start: 1685951466.498595 - stop: 1685951466.499137 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] 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pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]') - keywords: {'test_argparse_append_with_default[job_order1-expected_values1]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order1-expected_values1': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")] - duration: 0.0003429710004638764 - start: 1685951467.345119 - stop: 1685951467.345463 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order2-expected_values2] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order2-expected_values2]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> ['--file_paths', '/home/bart/cwl_test/test2', '--file_paths', '/home/bart/cwl_test/test3'] [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> ['/home/bart/cwl_test/test2', '/home/bart/cwl_test/test3'] [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order2-expected_values2] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order2-expected_values2]') - keywords: {'test_argparse_append_with_default[job_order2-expected_values2]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order2-expected_values2': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0004941550005241879 - start: 1685951467.347192 - stop: 1685951467.347687 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order2-expected_values2] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order2-expected_values2]') - keywords: {'test_argparse_append_with_default[job_order2-expected_values2]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order2-expected_values2': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")] - duration: 0.0167755689999467 - start: 1685951467.3482409 - stop: 1685951467.3650181 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order2-expected_values2] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order2-expected_values2]') - keywords: {'test_argparse_append_with_default[job_order2-expected_values2]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order2-expected_values2': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/default_values_list.cwl'")] - duration: 0.0003022480004801764 - start: 1685951467.365503 - stop: 1685951467.365806 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order2-expected_values2] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order2-expected_values2]') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js - location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js - location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') - keywords: {'test_js_hint_reports_invalid_js': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00031787399984750664 - start: 1685951467.368246 - stop: 1685951467.368565 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js - location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') - keywords: {'test_js_hint_reports_invalid_js': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.013302664000548248 - start: 1685951467.369011 - stop: 1685951467.382315 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js - location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') - keywords: {'test_js_hint_reports_invalid_js': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0002095480003845296 - start: 1685951467.3827882 - stop: 1685951467.3830001 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_validate_js.py::test_js_hint_reports_invalid_js - location: ('tests/test_validate_js.py', 66, 'test_js_hint_reports_invalid_js') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_validate_js.py::test_js_hint_warn_on_es6 - location: ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_js_hint_warn_on_es6 - location: ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6') - keywords: {'test_js_hint_warn_on_es6': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0002407930005574599 - start: 1685951467.385212 - stop: 1685951467.3854542 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_js_hint_warn_on_es6 - location: ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6') - keywords: {'test_js_hint_warn_on_es6': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [] - duration: 0.008448042999589234 - start: 1685951467.386027 - stop: 1685951467.394476 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_validate_js.py::test_js_hint_warn_on_es6 - location: ('tests/test_validate_js.py', 70, 'test_js_hint_warn_on_es6') - keywords: {'test_js_hint_warn_on_es6': 1, 'test_validate_js.py': 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pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x1092a7730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_windows_warning.py::test_windows_warning - location: ('tests/test_windows_warning.py', 12, 'test_windows_warning') - keywords: {'test_windows_warning': 1, 'test_windows_warning.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.004307549000259314 - start: 1685951467.426868 - stop: 1685951467.431178 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_windows_warning.py::test_windows_warning - location: ('tests/test_windows_warning.py', 12, 'test_windows_warning') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - finish pytest_runtestloop --> True [hook] - pytest_sessionfinish [hook] - session: testsfailed=2 testscollected=664> - exitstatus: 1 - finish pytest_sessionfinish --> [] [hook] - pytest_unconfigure [hook] - config: <_pytest.config.Config object at 0x1092a7730> - finish pytest_unconfigure --> [] [hook] -_research_object_picklability' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_research_object_picklability - location: ('tests/test_provenance.py', 788, 'test_research_object_picklability') - keywords: {'test_research_object_picklability': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj')] - duration: 0.00234540899964486 - start: 1685951451.797377 - stop: 1685951451.799724 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_research_object_picklability - location: ('tests/test_provenance.py', 788, 'test_research_object_picklability') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_directory_workflow_no_listing - location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_directory_workflow_no_listing - location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') - keywords: {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0016229729999395204 - start: 1685951451.801435 - stop: 1685951451.80306 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - early skip of rewriting module: encodings.ascii [assertion] - early skip of rewriting module: rdflib.plugins.parsers.jsonld [assertion] - early skip of rewriting module: rdflib.plugins.shared [assertion] - early skip of rewriting module: rdflib.plugins.shared.jsonld [assertion] - early skip of rewriting module: rdflib.plugins.shared.jsonld.context [assertion] - early skip of rewriting module: rdflib.plugins.shared.jsonld.errors [assertion] - early skip of rewriting module: rdflib.plugins.shared.jsonld.keys [assertion] - early skip of rewriting module: rdflib.plugins.shared.jsonld.util [assertion] - early skip of rewriting module: rdflib.plugins.serializers [assertion] - early skip of rewriting module: rdflib.plugins.serializers.turtle [assertion] - early skip of rewriting module: prov.serializers.provjson [assertion] - early skip of rewriting module: prov.serializers.provn [assertion] - early skip of rewriting module: prov.serializers.provxml [assertion] - early skip of rewriting module: prov.serializers.provrdf [assertion] - early skip of rewriting module: rdflib.plugins.serializers.nt [assertion] - early skip of rewriting module: rdflib.plugins.serializers.jsonld [assertion] - pytest_runtest_makereport [hook] - item: - call: > - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_directory_workflow_no_listing - location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') - keywords: {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: failed - longrepr: {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 891, 'message': "AssertionError: assert not True\n + where True = ()\n + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"}, 'reprtraceback': {'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_directory_workflow_no_listing(tmp_path: Path) -> None:', ' """', ' This test will check for 3 files that should be there and 3 files that should not be there.', ' @param tmp_path:', ' """', ' ', ' dir2 = tmp_path / "dir_deep_listing"', ' dir2.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in a b c ; do echo -n $x | sha1sum ; done', ' "a": "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",', ' "b": "e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",', ' "c": "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",', ' }', ' for x in "abc":', ' # Make test files with predictable hashes', ' with open(dir2 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir3 = tmp_path / "dir_no_listing"', ' dir3.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in d e f ; do echo -n $x | sha1sum ; done', ' "d": "3c363836cf4e16666669a25da280a1865c2d2874",', ' "e": "58e6b3a414a1e090dfc6029add0f3555ccba127f",', ' "f": "4a0a19218e082a343a1b17e5333409af9d98f0f5",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir3 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir4 = tmp_path / "dir_no_info"', ' dir4.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in g h i ; do echo -n $x | sha1sum ; done', ' "g": "54fd1711209fb1c0781092374132c66e79e2241b",', ' "h": "27d5482eebd075de44389774fce28c69f45c8a75",', ' "i": "042dc4512fa3d391c5170cf3aa61e6a638f84342",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir4 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/directory_no_listing.cwl"),', ' "--dir",', ' str(dir2),', ' "--ignore",', ' str(dir3),', ' "--ignore_no_info",', ' str(dir4),', ' )', ' ', ' # Visualize the path structure', ' list_files(tmp_path)', ' ', ' # check invert? as there should be no data in there', ' # check_provenance(folder, directory=True)', ' ', ' # Output should include ls stdout of filenames a b c on each line', ' file_list = (', ' folder', ' / "data"', ' / "84"', ' / "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4"', ' # checksum as returned from:', ' # echo -e "a\\nb\\nc" | sha1sum', ' # 3ca69e8d6c234a469d16ac28a4a658c92267c423 -', ' )', ' # File should not exist...', '> assert not file_list.is_file()', 'E AssertionError: assert not True', "E + where True = ()", "E + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 891, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, 'sections': [], 'chain': [({'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_directory_workflow_no_listing(tmp_path: Path) -> None:', ' """', ' This test will check for 3 files that should be there and 3 files that should not be there.', ' @param tmp_path:', ' """', ' ', ' dir2 = tmp_path / "dir_deep_listing"', ' dir2.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in a b c ; do echo -n $x | sha1sum ; done', ' "a": "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",', ' "b": "e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",', ' "c": "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",', ' }', ' for x in "abc":', ' # Make test files with predictable hashes', ' with open(dir2 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir3 = tmp_path / "dir_no_listing"', ' dir3.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in d e f ; do echo -n $x | sha1sum ; done', ' "d": "3c363836cf4e16666669a25da280a1865c2d2874",', ' "e": "58e6b3a414a1e090dfc6029add0f3555ccba127f",', ' "f": "4a0a19218e082a343a1b17e5333409af9d98f0f5",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir3 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' dir4 = tmp_path / "dir_no_info"', ' dir4.mkdir()', ' sha1 = {', ' # Expected hashes of ASCII letters (no linefeed)', ' # as returned from:', ' # for x in g h i ; do echo -n $x | sha1sum ; done', ' "g": "54fd1711209fb1c0781092374132c66e79e2241b",', ' "h": "27d5482eebd075de44389774fce28c69f45c8a75",', ' "i": "042dc4512fa3d391c5170cf3aa61e6a638f84342",', ' }', ' for x in "def":', ' # Make test files with predictable hashes', ' with open(dir4 / x, "w", encoding="ascii") as f:', ' f.write(x)', ' ', ' folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/directory_no_listing.cwl"),', ' "--dir",', ' str(dir2),', ' "--ignore",', ' str(dir3),', ' "--ignore_no_info",', ' str(dir4),', ' )', ' ', ' # Visualize the path structure', ' list_files(tmp_path)', ' ', ' # check invert? as there should be no data in there', ' # check_provenance(folder, directory=True)', ' ', ' # Output should include ls stdout of filenames a b c on each line', ' file_list = (', ' folder', ' / "data"', ' / "84"', ' / "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4"', ' # checksum as returned from:', ' # echo -e "a\\nb\\nc" | sha1sum', ' # 3ca69e8d6c234a469d16ac28a4a658c92267c423 -', ' )', ' # File should not exist...', '> assert not file_list.is_file()', 'E AssertionError: assert not True', "E + where True = ()", "E + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 891, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 891, 'message': "AssertionError: assert not True\n + where True = ()\n + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"}, None)]} - when: call - user_properties: [] - sections: [('Captured stdout call', '{\n "output_1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad"\n },\n "output_2": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0\ntest_directory_workflow_no_lis0/\n cwltool-run/\n 511f5ede99eeae60df68dedf0f5a3c2886774dad\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir_no_info/\n f\n d\n e\n dir_deep_listing/\n a\n c\n b\n dir_no_listing/\n f\n d\n e\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory_no_listing.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3c363836cf4e16666669a25da280a1865c2d2874\n 58/\n 58e6b3a414a1e090dfc6029add0f3555ccba127f\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n a0/\n a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n 4a/\n 4a0a19218e082a343a1b17e5333409af9d98f0f5\n metadata/\n directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n manifest.json\n directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n logs/\n engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/KKDWnh\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'--ignore\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'--ignore_no_info\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: bf9a8c91a428be6becd92c778c02c67d427411a8 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f63ffc058c8cfdb908506337c548afa6df073ae4c60dfd126529041314a548a5 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4fd8262b0744c271fe42c0c7a3142522708348559d0e405bb03bf2ab6becbeb7f64fecd3d8fb0762aa478fd99791200d9c3503e2e2e47b16546bd96fda2bca33 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing"\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}, \'ignore\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}, \'ignore_no_info\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_deep_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_info\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: b8ccdd89c80eca48567812797b860122d330b485 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: c1d4042283d1ce80021fa05c18eed2ae1bffea933f49ddd960b4a09f9a262cb5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: bdc150fa3761c3d002efb9be43f71cf8dac2e1f42259fdff201f185d0603839f2b882baf2cf28656ecfdfa1519fdf92a6b8611fab87b17604c45c09e28ed72ee workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ba113d80556b23c15fd7c2455789b16fe31f2335 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9ae22ea23ca80ffebd84f7e8ff4b640ec2d0f1956c56555485252b0f43892ce6 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 2b38d01f508e3abb2d8249e19be4d222e1b13c37943489f70523fa076f09d012a4f139a3b480706cd411ec961a4f8dcb5b255404f7f71fa74a24bf1886f66889 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 4a0a19218e082a343a1b17e5333409af9d98f0f5 data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 3c363836cf4e16666669a25da280a1865c2d2874 data/3c/3c363836cf4e16666669a25da280a1865c2d2874\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 58e6b3a414a1e090dfc6029add0f3555ccba127f data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 2de598f6b273e2eaaabca9703f0ca739ac4fb4bd metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 803eefe7af4871fc1029330cf00afb4abc33e44591400b6036c887ce4d3516c8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 26f9234c3e7852c13da1a41405bba99f80817d45abf0beed442c3c31cd106afb3b4bdc96fced5ce6e84194af3d156b1c880cef95d9283e3a98f6a87af04e40b8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 94788d2e8451e82a089085ce9a13d21d7648a56a metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: be9b32c701e852c1cce196ed17bb7d04ce147cda1847a2bb31b81a0b3b3bdfb8 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 7f08203a26bde01dd72f0888a87167b6ac571b24e88928de1d73b3cdfcd873e5576f2ccb107b88fa663be20691607e6c74c57f73e2ab5acfa2da3ab1242a5465 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info",\n "basename": "dir_no_info"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from _:c64797b9-0e72-438b-b250-9a183c2486c6 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a01f4d65bf45da813bc5c1482c403b467537faba metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b68aeee0d249094334ad30ea74bf2e8e13de8620ffba8d87dd4ff03f4f707c9 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 0508e90f315884b3b5652850fe11970d60be330ecc6079e443b6f9cf8cdd539ccd6f0f679d05b0ee5c9da1550a3ca81b79425c9b07bca981a24338d10441f318 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 456e3bd591c3db18d15eb03f1b0033f71af12d3a metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 0b6bb416adfdfd452957e1ece6c05a5065835bb85234d7946a264c4016248028 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 856999b9b5ec46248fac41601440d838ba31b12e7c942005522d5e3ef91ebc7edd707457acdfc7d46895a185beb5785592c34d596e22cfb805edc527fc62a209 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9c22bec2e40d921fa850aa5fff207217b2700033 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f8c81c1297aa21b9e5e6d72fbdd4d5bb4dbc5fcc7a8332e4eb07cc6af6620171 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 59200606c8f78dec7b9c4ee540aa62a420c89b773788766589cc20849df29bc5ad624c61cd642b3eb214ab9d94598f99d290690e5e9668690398e7fee40211c3 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmpuu8p9qg8\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmpgouh1jdv\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from _:6798550b-35c6-4878-b539-969960c2ddd6 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "Directory",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n }\n ],\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f"\n }\n },\n {\n "position": [\n 2,\n "ignore"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing",\n "path": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "dirname": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 8cc5feedb2b21504d21859e0f63631f0b517553b metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b0f753abd9f52fa7bda09156130e6b0b936f1cd0705a6894db0eadff26b12a1 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: d6d5e13b344294994185ebcff17d42825d055b22a1e88978298377197522f2542db43987450874f4fd8da234a974070ce23ac03eff61c0a5a647d4c97a68cec6 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 18386d0fde6d11e92ff3eb4475f6553b3093c775 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 31c7501fcee1311e24b50b4142dc0321239dbdaaf821e84c7370321898b234d3 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: be3cf5fc2ba70daafbc4cfe1fe3dd41ee9772f0cccd8f955aa6b0c619abb9eda2bc00818090ad245ffe663fb8151f5b965feb7f4933e3ce68e7d38ff89aa3587 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: a0ce0441f957dcde10291470aa5062ffc7cbdf8c data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "output_1": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n },\n "output_2": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmphgdo2k_m\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmpy12k7j25\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp30294ykg/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe4wl6xjm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp30294ykg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp03q_qnzm\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 831d591ea563d82200f6b29cdbed89958af99946 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8591aab1f32872e19f186118be1462101272c003e5725780ad0a1053b4f45b8 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 1b73e532287cafb4438cfc69dd62ca998d374d25d2d2a9e1aae2d80da74193ec8abc5494227ed037b4a9cbcebd72b4ba2f5c5a995fc9406ad87abc08a421237a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 52917a96deb1331e4f3e0d0c0ca5c06da11b550f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 952621e5f975fa4b8536d1246e03019673efe29716be7dd946885b26420ad858 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 9d13a8b2e9919c7d90a5b65c0af7326c4869efebe2b1525d1dee1d573159349fa8c3d9a06386e6e3054b4517ac86f5389bb90d9cc8105857baa9a142a9958123 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 4660384a529ef8217263414cfe7d8e09a36dae6a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8d43e02f50436e6bc3d92fdf3f37d0452a90fb55cc177c4902b62802ce733b8 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: c3a8205627d56adebcf5e2221b0ce6adc18bebc2af049dbec6dd744c90d1d704cca928860c5b41a8c0fa7056484ca8a454555ab058b982a5a5b3c4b48e35de1d metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: de4b6608f9e3af201c70ff6b53f85749a8492405 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: fadae5349308a66d763eacbe40b6c0348bdfd6947a138a8f8adab6c451836db5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4eb4037e059930960700522093a233245189d1e1284b785d7642142d07ace00ecb89da2a98af756469be68dec3c3b6b0e41368ad4b0325b536fffb642fdc0280 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 153127a4ee5a028d1acd636b0809d434d53da02d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 717a4f8ae33902dcd217991e923892a59b626fe60f616d3cd275806d18e9da4a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 5c8ece230a9c9d65f0b953c27045f92d27e3d6ecc3823e7ef9d3cb4426d66ded6a1fddd45a4bfed846940ed9a1f4bc3f4e9159650a856e9c7bdde1a7162f4ead metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9a047fa31e52f7b66c1a7cebf88c57d9e388c8c6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: a727a73f4d563af8f90316d9ec809d0f853abc53632d2f306ca2944475293cdc metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 83f351fed5f621fa4763e6d0f0762964aa213f325926bf7c406e94eef34970695b9c599bfbd807565b497858edbdfbacc1c3001cbdfb54bb826e49da09ee004f metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'output_1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}, \'output_2\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': 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\'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a259a2ddea0fb8dbe04ce95431c7b87d74444c8d workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f92dbdf72304f179e312894c469c59f4b08ddabf26264f1ad7a38aa6a527b39e workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 586e6634367c1f8cddf3f26d6e2c7ff826ce3677902c23890028d73f66b854b30eb013b70cecaefb3fdcb8f47fe266e7182f62f24b6f5d94973d73b7dbc04479 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 757937dc88f5d446a6e63c9d1f12acde32b02ecd snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 2c725914f45b19c49b5a6e9540477b70a0273cefdbd82c19de19054de16cb24f snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6d058c8a26fad02c7935f0ee249b186701f49d64ed43f8dccc87ca2f374356b971470006906e36f6d9c888cf50ead1e3fe3f6759e8d1d53a678ca6c1a171387a snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ec85041b357ff2b39338cfbc69d2560640966f89 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 36a504d2c4551667e228d84c4eed90bd73747fe98606b30d912ec9b1ec3767bd metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: f2e20d11de50af96dc8e3bfcd43f0bc8d78342dda00c88c80de92a8f04d4aa3bbf684bf7c59f342cb8ef84393e00327a65b1c107d18f4a449e6116496d5e1f54 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0033518ae68cb74ef1d56196451d0ac9957ce80f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 640cf34ac826eeba52a190d69e5d9f3e0cd8025e6c6a20a5c32c5a479c687c67 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6345ca41b6e0eedc5d3dc2a171ce96cb26aef6a6072f27634478eee2492ac756794ece6fd4949d827a922b55d0d2d7fd5c66b69ade15549c3b96aef4b86e9d0a metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0d2331dab4d408bceb1057cfe5f1e826e1990c29 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 37908e47bb9f9ca212410631fd36ca1f333b9640b281b15639bfc1a822730ba6 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 059ed78b311c6402fb86010caf6283f0bd799fc922264bbef8b82bfb774e14680d16ee89810d4a50f82511d03a2a7596afe8806d3137f4c749d9db1e3b533ca2 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance')] - duration: 4.963674428999184 - start: 1685951451.80366 - stop: 1685951456.767212 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_exception_interact [hook] - node: - call: > - report: - finish pytest_exception_interact --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_provenance.py::test_directory_workflow_no_listing - location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') - keywords: {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '{\n "output_1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad"\n },\n "output_2": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0\ntest_directory_workflow_no_lis0/\n cwltool-run/\n 511f5ede99eeae60df68dedf0f5a3c2886774dad\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir_no_info/\n f\n d\n e\n dir_deep_listing/\n a\n c\n b\n dir_no_listing/\n f\n d\n e\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory_no_listing.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3c363836cf4e16666669a25da280a1865c2d2874\n 58/\n 58e6b3a414a1e090dfc6029add0f3555ccba127f\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n a0/\n a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n 4a/\n 4a0a19218e082a343a1b17e5333409af9d98f0f5\n metadata/\n directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n manifest.json\n directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n logs/\n engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/KKDWnh\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'--ignore\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'--ignore_no_info\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: bf9a8c91a428be6becd92c778c02c67d427411a8 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f63ffc058c8cfdb908506337c548afa6df073ae4c60dfd126529041314a548a5 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4fd8262b0744c271fe42c0c7a3142522708348559d0e405bb03bf2ab6becbeb7f64fecd3d8fb0762aa478fd99791200d9c3503e2e2e47b16546bd96fda2bca33 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing"\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}, \'ignore\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}, \'ignore_no_info\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_deep_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_info\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: b8ccdd89c80eca48567812797b860122d330b485 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: c1d4042283d1ce80021fa05c18eed2ae1bffea933f49ddd960b4a09f9a262cb5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: bdc150fa3761c3d002efb9be43f71cf8dac2e1f42259fdff201f185d0603839f2b882baf2cf28656ecfdfa1519fdf92a6b8611fab87b17604c45c09e28ed72ee workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ba113d80556b23c15fd7c2455789b16fe31f2335 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9ae22ea23ca80ffebd84f7e8ff4b640ec2d0f1956c56555485252b0f43892ce6 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 2b38d01f508e3abb2d8249e19be4d222e1b13c37943489f70523fa076f09d012a4f139a3b480706cd411ec961a4f8dcb5b255404f7f71fa74a24bf1886f66889 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 4a0a19218e082a343a1b17e5333409af9d98f0f5 data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 3c363836cf4e16666669a25da280a1865c2d2874 data/3c/3c363836cf4e16666669a25da280a1865c2d2874\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 58e6b3a414a1e090dfc6029add0f3555ccba127f data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 2de598f6b273e2eaaabca9703f0ca739ac4fb4bd metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 803eefe7af4871fc1029330cf00afb4abc33e44591400b6036c887ce4d3516c8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 26f9234c3e7852c13da1a41405bba99f80817d45abf0beed442c3c31cd106afb3b4bdc96fced5ce6e84194af3d156b1c880cef95d9283e3a98f6a87af04e40b8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 94788d2e8451e82a089085ce9a13d21d7648a56a metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: be9b32c701e852c1cce196ed17bb7d04ce147cda1847a2bb31b81a0b3b3bdfb8 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 7f08203a26bde01dd72f0888a87167b6ac571b24e88928de1d73b3cdfcd873e5576f2ccb107b88fa663be20691607e6c74c57f73e2ab5acfa2da3ab1242a5465 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info",\n "basename": "dir_no_info"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from _:c64797b9-0e72-438b-b250-9a183c2486c6 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a01f4d65bf45da813bc5c1482c403b467537faba metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b68aeee0d249094334ad30ea74bf2e8e13de8620ffba8d87dd4ff03f4f707c9 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 0508e90f315884b3b5652850fe11970d60be330ecc6079e443b6f9cf8cdd539ccd6f0f679d05b0ee5c9da1550a3ca81b79425c9b07bca981a24338d10441f318 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 456e3bd591c3db18d15eb03f1b0033f71af12d3a metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 0b6bb416adfdfd452957e1ece6c05a5065835bb85234d7946a264c4016248028 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 856999b9b5ec46248fac41601440d838ba31b12e7c942005522d5e3ef91ebc7edd707457acdfc7d46895a185beb5785592c34d596e22cfb805edc527fc62a209 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9c22bec2e40d921fa850aa5fff207217b2700033 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f8c81c1297aa21b9e5e6d72fbdd4d5bb4dbc5fcc7a8332e4eb07cc6af6620171 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 59200606c8f78dec7b9c4ee540aa62a420c89b773788766589cc20849df29bc5ad624c61cd642b3eb214ab9d94598f99d290690e5e9668690398e7fee40211c3 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmpuu8p9qg8\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmpgouh1jdv\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from _:6798550b-35c6-4878-b539-969960c2ddd6 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "Directory",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n }\n ],\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f"\n }\n },\n {\n "position": [\n 2,\n "ignore"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing",\n "path": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "dirname": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 8cc5feedb2b21504d21859e0f63631f0b517553b metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b0f753abd9f52fa7bda09156130e6b0b936f1cd0705a6894db0eadff26b12a1 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: d6d5e13b344294994185ebcff17d42825d055b22a1e88978298377197522f2542db43987450874f4fd8da234a974070ce23ac03eff61c0a5a647d4c97a68cec6 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 18386d0fde6d11e92ff3eb4475f6553b3093c775 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 31c7501fcee1311e24b50b4142dc0321239dbdaaf821e84c7370321898b234d3 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: be3cf5fc2ba70daafbc4cfe1fe3dd41ee9772f0cccd8f955aa6b0c619abb9eda2bc00818090ad245ffe663fb8151f5b965feb7f4933e3ce68e7d38ff89aa3587 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: a0ce0441f957dcde10291470aa5062ffc7cbdf8c data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "output_1": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n },\n "output_2": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmphgdo2k_m\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmpy12k7j25\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp30294ykg/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe4wl6xjm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp30294ykg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp03q_qnzm\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 831d591ea563d82200f6b29cdbed89958af99946 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8591aab1f32872e19f186118be1462101272c003e5725780ad0a1053b4f45b8 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 1b73e532287cafb4438cfc69dd62ca998d374d25d2d2a9e1aae2d80da74193ec8abc5494227ed037b4a9cbcebd72b4ba2f5c5a995fc9406ad87abc08a421237a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 52917a96deb1331e4f3e0d0c0ca5c06da11b550f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 952621e5f975fa4b8536d1246e03019673efe29716be7dd946885b26420ad858 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 9d13a8b2e9919c7d90a5b65c0af7326c4869efebe2b1525d1dee1d573159349fa8c3d9a06386e6e3054b4517ac86f5389bb90d9cc8105857baa9a142a9958123 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 4660384a529ef8217263414cfe7d8e09a36dae6a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8d43e02f50436e6bc3d92fdf3f37d0452a90fb55cc177c4902b62802ce733b8 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: c3a8205627d56adebcf5e2221b0ce6adc18bebc2af049dbec6dd744c90d1d704cca928860c5b41a8c0fa7056484ca8a454555ab058b982a5a5b3c4b48e35de1d metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: de4b6608f9e3af201c70ff6b53f85749a8492405 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: fadae5349308a66d763eacbe40b6c0348bdfd6947a138a8f8adab6c451836db5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4eb4037e059930960700522093a233245189d1e1284b785d7642142d07ace00ecb89da2a98af756469be68dec3c3b6b0e41368ad4b0325b536fffb642fdc0280 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 153127a4ee5a028d1acd636b0809d434d53da02d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 717a4f8ae33902dcd217991e923892a59b626fe60f616d3cd275806d18e9da4a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 5c8ece230a9c9d65f0b953c27045f92d27e3d6ecc3823e7ef9d3cb4426d66ded6a1fddd45a4bfed846940ed9a1f4bc3f4e9159650a856e9c7bdde1a7162f4ead metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9a047fa31e52f7b66c1a7cebf88c57d9e388c8c6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: a727a73f4d563af8f90316d9ec809d0f853abc53632d2f306ca2944475293cdc metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 83f351fed5f621fa4763e6d0f0762964aa213f325926bf7c406e94eef34970695b9c599bfbd807565b497858edbdfbacc1c3001cbdfb54bb826e49da09ee004f metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'output_1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}, \'output_2\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 153\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a259a2ddea0fb8dbe04ce95431c7b87d74444c8d workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f92dbdf72304f179e312894c469c59f4b08ddabf26264f1ad7a38aa6a527b39e workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 586e6634367c1f8cddf3f26d6e2c7ff826ce3677902c23890028d73f66b854b30eb013b70cecaefb3fdcb8f47fe266e7182f62f24b6f5d94973d73b7dbc04479 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 757937dc88f5d446a6e63c9d1f12acde32b02ecd snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 2c725914f45b19c49b5a6e9540477b70a0273cefdbd82c19de19054de16cb24f snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6d058c8a26fad02c7935f0ee249b186701f49d64ed43f8dccc87ca2f374356b971470006906e36f6d9c888cf50ead1e3fe3f6759e8d1d53a678ca6c1a171387a snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ec85041b357ff2b39338cfbc69d2560640966f89 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 36a504d2c4551667e228d84c4eed90bd73747fe98606b30d912ec9b1ec3767bd metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: f2e20d11de50af96dc8e3bfcd43f0bc8d78342dda00c88c80de92a8f04d4aa3bbf684bf7c59f342cb8ef84393e00327a65b1c107d18f4a449e6116496d5e1f54 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0033518ae68cb74ef1d56196451d0ac9957ce80f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 640cf34ac826eeba52a190d69e5d9f3e0cd8025e6c6a20a5c32c5a479c687c67 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6345ca41b6e0eedc5d3dc2a171ce96cb26aef6a6072f27634478eee2492ac756794ece6fd4949d827a922b55d0d2d7fd5c66b69ade15549c3b96aef4b86e9d0a metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0d2331dab4d408bceb1057cfe5f1e826e1990c29 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 37908e47bb9f9ca212410631fd36ca1f333b9640b281b15639bfc1a822730ba6 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 059ed78b311c6402fb86010caf6283f0bd799fc922264bbef8b82bfb774e14680d16ee89810d4a50f82511d03a2a7596afe8806d3137f4c749d9db1e3b533ca2 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance')] - duration: 0.00152142999922944 - start: 1685951456.977313 - stop: 1685951456.978837 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_directory_workflow_no_listing - location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - nodeid: tests/test_provenance.py::test_directory_workflow_no_listing - when: runtest - location: None - finish pytest_warning_recorded --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print - location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print - location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') - keywords: {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0003581160008252482 - start: 1685951456.985954 - stop: 1685951456.986314 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print - location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') - keywords: {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '@prefix CommandLineBinding: .\n@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n cwl:inputBinding [ CommandLineBinding:position 1 ] ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'")] - duration: 0.6995283690002907 - start: 1685951456.986822 - stop: 1685951457.686334 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print - location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') - keywords: {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '@prefix CommandLineBinding: .\n@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n cwl:inputBinding [ CommandLineBinding:position 1 ] ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'")] - duration: 0.00019048600006499328 - start: 1685951457.686794 - stop: 1685951457.686985 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print - location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print_unicode - location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x10db8d870> [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print_unicode - location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') - keywords: {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0005043370001658332 - start: 1685951457.688944 - stop: 1685951457.68945 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print_unicode - location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') - keywords: {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stdout call', '@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix rdfs: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n rdfs:label "Sequence file in FASTA format" ;\n rdfs:comment """Input sequence file in FASTA format (not compressed/zipped!).\nCan be an assembled genome (genome mode) or transcriptome (DNA,\ntranscriptome mode), or protein sequences from an annotated gene set\n(proteins mode).\nNB: select just one transcript/protein per gene for your input,\notherwise they will appear as ‘Duplicated’ matches.\n""" ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m /Users/jasperk/gitlab/cwltool/cwltool/__main__.py 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl'\n")] - duration: 1.9449515790001897 - start: 1685951457.6899168 - stop: 1685951459.634825 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print_unicode - location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') - keywords: {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stdout call', '@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix rdfs: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n rdfs:label "Sequence file in FASTA format" ;\n rdfs:comment """Input sequence file in FASTA format (not compressed/zipped!).\nCan be an assembled genome (genome mode) or transcriptome (DNA,\ntranscriptome mode), or protein sequences from an annotated gene set\n(proteins mode).\nNB: select just one transcript/protein per gene for your input,\notherwise they will appear as ‘Duplicated’ matches.\n""" ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m /Users/jasperk/gitlab/cwltool/cwltool/__main__.py 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl'\n")] - duration: 0.0006568690005224198 - start: 1685951459.6365361 - stop: 1685951459.637194 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print_unicode - location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_singularity.py::test_singularity_iwdr - location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_singularity_iwdr0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_singularity_iwdr0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x10db8d3f0> [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_singularity.py::test_singularity_iwdr - location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') - keywords: {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.002171388000533625 - start: 1685951459.638792 - stop: 1685951459.6409652 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_singularity.py::test_singularity_iwdr - location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') - keywords: {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:810 Singularity error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 771, in run\n self.get_from_requirements(\n File "/Users/jasperk/gitlab/cwltool/cwltool/singularity.py", line 292, in get_from_requirements\n raise WorkflowException("singularity executable is not available")\ncwltool.errors.WorkflowException: singularity executable is not available\nERROR cwltool:main.py:1373 Workflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available')] - duration: 0.7381495270001324 - start: 1685951459.641752 - stop: 1685951460.379884 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_singularity.py::test_singularity_iwdr - location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') - keywords: {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:810 Singularity error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 771, in run\n self.get_from_requirements(\n File "/Users/jasperk/gitlab/cwltool/cwltool/singularity.py", line 292, in get_from_requirements\n raise WorkflowException("singularity executable is not available")\ncwltool.errors.WorkflowException: singularity executable is not available\nERROR cwltool:main.py:1373 Workflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available')] - duration: 0.00043232999996689614 - start: 1685951460.380364 - stop: 1685951460.3807979 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_singularity.py::test_singularity_iwdr - location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull - location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_runtest_makereport [hook] - item: - call: > - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull - location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') - keywords: {'test_singularity_incorrect_image_pull': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: skipped - longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 84, 'Skipped: Requires the singularity executable on the system path.') - when: setup - user_properties: [] - sections: [] - duration: 0.00022189900028024567 - start: 1685951460.381962 - stop: 1685951460.382185 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull - location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') - keywords: {'test_singularity_incorrect_image_pull': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.00021053000000392785 - start: 1685951460.382848 - stop: 1685951460.38306 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull - location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_singularity.py::test_singularity_local - location: ('tests/test_singularity.py', 98, 'test_singularity_local') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_runtest_makereport [hook] - item: - call: > - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_singularity.py::test_singularity_local - location: ('tests/test_singularity.py', 98, 'test_singularity_local') - keywords: {'test_singularity_local': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: skipped - longrepr: ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 99, 'Skipped: Requires the singularity executable on the system path.') - when: setup - user_properties: [] - sections: [] - duration: 0.0002089989993692143 - start: 1685951460.385066 - stop: 1685951460.3852758 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_singularity.py::test_singularity_local - location: ('tests/test_singularity.py', 98, 'test_singularity_local') - keywords: {'test_singularity_local': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [] - duration: 0.0002950230000351439 - start: 1685951460.38608 - stop: 1685951460.3863769 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_singularity.py::test_singularity_local - location: ('tests/test_singularity.py', 98, 'test_singularity_local') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step - location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step - location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') - keywords: {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.001556540999445133 - start: 1685951460.3884459 - stop: 1685951460.390004 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step - location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') - keywords: {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp65j863ig$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp65j863ig/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp65j863ig/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmp11jtljvb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpwn42k8_w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp65j863ig/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp65j863ig\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 1.1143909949996669 - start: 1685951460.390568 - stop: 1685951461.5049338 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step - location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') - keywords: {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp65j863ig$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp65j863ig/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp65j863ig/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmp11jtljvb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpwn42k8_w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp65j863ig/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp65j863ig\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0006726860001435853 - start: 1685951461.506804 - stop: 1685951461.507478 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step - location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step - location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0 [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step - location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') - keywords: {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.0021509959997274564 - start: 1685951461.510327 - stop: 1685951461.512479 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step - location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') - keywords: {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\'\nDEBUG cwltool:command_line_tool.py:982 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json#count-lines17-wf/step1/run/count-lines17-wf.cwl@step_step1@run/stepX/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run/stepY/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run\nDEBUG cwltool:command_line_tool.py:988 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initial work dir {}\nINFO cwltool:job.py:266 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] /private/tmp/docker_tmp_9yt0z8_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_9yt0z8_,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmprz9dykzk,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpsbmfwops/20230605095102-600646.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt > /private/tmp/docker_tmp_9yt0z8_/output\nINFO cwltool:job.py:905 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] completed success\nDEBUG cwltool:job.py:422 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_9yt0z8_/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing input staging directory /private/tmp/docker_tmp89udep8a\nDEBUG cwltool:job.py:454 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing temporary directory /private/tmp/docker_tmprz9dykzk\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_9yt0z8_/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_9yt0z8_\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 2.11600468800043 - start: 1685951461.5130591 - stop: 1685951463.6290119 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step - location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') - keywords: {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\'\nDEBUG cwltool:command_line_tool.py:982 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json#count-lines17-wf/step1/run/count-lines17-wf.cwl@step_step1@run/stepX/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run/stepY/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run\nDEBUG cwltool:command_line_tool.py:988 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initial work dir {}\nINFO cwltool:job.py:266 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] /private/tmp/docker_tmp_9yt0z8_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_9yt0z8_,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmprz9dykzk,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpsbmfwops/20230605095102-600646.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt > /private/tmp/docker_tmp_9yt0z8_/output\nINFO cwltool:job.py:905 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] completed success\nDEBUG cwltool:job.py:422 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_9yt0z8_/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing input staging directory /private/tmp/docker_tmp89udep8a\nDEBUG cwltool:job.py:454 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing temporary directory /private/tmp/docker_tmprz9dykzk\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_9yt0z8_/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_9yt0z8_\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.0008782109998719534 - start: 1685951463.630854 - stop: 1685951463.6317341 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step - location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value - location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value - location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') - keywords: {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.00043156799983989913 - start: 1685951463.634976 - stop: 1685951463.6354098 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value - location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') - keywords: {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', 'latest: Pulling from library/alpine\nDigest: sha256:02bb6f428431fbc2809c5d1b41eab5a68350194fb508869a33cb1af4444c9b11\nStatus: Image is up to date for alpine:latest\ndocker.io/library/alpine:latest\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:argparser.py:943 Can\'t make command line argument from Any\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "message": "two"\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step task2\nDEBUG cwltool:workflow_job.py:727 [step task2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2] start\nDEBUG cwltool:command_line_tool.py:982 [job task2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2\nDEBUG cwltool:command_line_tool.py:988 [job task2] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/alpine:latest\']\nDEBUG cwltool:job.py:215 [job task2] initial work dir {}\nINFO cwltool:job.py:266 [job task2] /private/tmp/docker_tmp2vpjz9j3$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2vpjz9j3,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpbyyklcxx,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpwtgdio32/20230605095106-754192.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2] completed success\nDEBUG cwltool:job.py:422 [job task2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2vpjz9j3/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {}\nDEBUG cwltool:job.py:446 [job task2] Removing input staging directory /private/tmp/docker_tmpy2a25zaq\nDEBUG cwltool:job.py:454 [job task2] Removing temporary directory /private/tmp/docker_tmpbyyklcxx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2vpjz9j3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpysive81g\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 4.140258484999322 - start: 1685951463.636079 - stop: 1685951467.776237 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value - location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') - keywords: {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', 'latest: Pulling from library/alpine\nDigest: sha256:02bb6f428431fbc2809c5d1b41eab5a68350194fb508869a33cb1af4444c9b11\nStatus: Image is up to date for alpine:latest\ndocker.io/library/alpine:latest\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:argparser.py:943 Can\'t make command line argument from Any\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "message": "two"\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step task2\nDEBUG cwltool:workflow_job.py:727 [step task2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2] start\nDEBUG cwltool:command_line_tool.py:982 [job task2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2\nDEBUG cwltool:command_line_tool.py:988 [job task2] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/alpine:latest\']\nDEBUG cwltool:job.py:215 [job task2] initial work dir {}\nINFO cwltool:job.py:266 [job task2] /private/tmp/docker_tmp2vpjz9j3$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2vpjz9j3,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpbyyklcxx,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpwtgdio32/20230605095106-754192.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2] completed success\nDEBUG cwltool:job.py:422 [job task2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2vpjz9j3/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {}\nDEBUG cwltool:job.py:446 [job task2] Removing input staging directory /private/tmp/docker_tmpy2a25zaq\nDEBUG cwltool:job.py:454 [job task2] Removing temporary directory /private/tmp/docker_tmpbyyklcxx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2vpjz9j3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpysive81g\nINFO cwltool:main.py:1366 Final process status is success')] - duration: 0.00046557099994970486 - start: 1685951467.777664 - stop: 1685951467.778131 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value - location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - pytest_runtest_protocol [hook] - item: - nextitem: None - pytest_runtest_logstart [hook] - nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix - location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_setup [hook] - item: - pytest_fixture_setup [hook] - fixturedef: - request: > - mktemp /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0 [config:tmpdir] - finish pytest_fixture_setup --> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0 [hook] - pytest_fixture_setup [hook] - fixturedef: - request: > - finish pytest_fixture_setup --> <_pytest.monkeypatch.MonkeyPatch object at 0x10d56f1c0> [hook] - finish pytest_runtest_setup --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix - location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') - keywords: {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: setup - user_properties: [] - sections: [] - duration: 0.002130539000063436 - start: 1685951467.780889 - stop: 1685951467.783021 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_call [hook] - item: - pytest_pyfunc_call [hook] - pyfuncitem: - finish pytest_pyfunc_call --> True [hook] - finish pytest_runtest_call --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix - location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') - keywords: {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: call - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']\n"), ('Captured log call', "INFO cwltool:docker.py:164 ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']")] - duration: 0.09524703099941689 - start: 1685951467.7836092 - stop: 1685951467.878856 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_teardown [hook] - item: - nextitem: None - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - pytest_fixture_post_finalizer [hook] - fixturedef: - request: > - finish pytest_fixture_post_finalizer --> [] [hook] - finish pytest_runtest_teardown --> [] [hook] - pytest_runtest_makereport [hook] - item: - call: - finish pytest_runtest_makereport --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_report_teststatus --> ('', '', '') [hook] - pytest_report_to_serializable [hook] - config: <_pytest.config.Config object at 0x10a90b730> - report: - finish pytest_report_to_serializable --> [hook] - nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix - location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') - keywords: {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1} - outcome: passed - longrepr: None - when: teardown - user_properties: [] - sections: [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']\n"), ('Captured log call', "INFO cwltool:docker.py:164 ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']")] - duration: 0.003588997999941057 - start: 1685951467.880084 - stop: 1685951467.8836741 - $report_type: TestReport - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix - location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') - finish pytest_runtest_logfinish --> [] [hook] - finish pytest_runtest_protocol --> True [hook] - finish pytest_runtestloop --> True [hook] - pytest_sessionfinish [hook] - session: testsfailed=1 testscollected=664> - exitstatus: 1 - finish pytest_sessionfinish --> [] [hook] - pytest_unconfigure [hook] - config: <_pytest.config.Config object at 0x10a90b730> - finish pytest_unconfigure --> [] [hook] -f80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_listing_v1_0', 'location': ('tests/test_ext.py', 63, 'test_listing_v1_0'), 'keywords': {'test_listing_v1_0': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl'\n\x1b[1;30mINFO\x1b[0m [job listing_v1_0.cwl] /private/tmp/docker_tmp48ro06s9$ echo \\\n /private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\n/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\n\x1b[1;30mINFO\x1b[0m [job listing_v1_0.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job listing_v1_0.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\nDEBUG cwltool:command_line_tool.py:988 [job listing_v1_0.cwl] {\n "d": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1",\n "basename": "tmp1",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2",\n "basename": "tmp2",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3",\n "basename": "tmp3",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep",\n "basename": ".gitkeep",\n "size": 0\n }\n ]\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job listing_v1_0.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3/.gitkeep",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job listing_v1_0.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.d.listing[0].listing[0])"\n }\n]\nDEBUG cwltool:job.py:215 [job listing_v1_0.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job listing_v1_0.cwl] /private/tmp/docker_tmp48ro06s9$ echo \\\n /private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job listing_v1_0.cwl] completed success\nDEBUG cwltool:job.py:422 [job listing_v1_0.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job listing_v1_0.cwl] Removing input staging directory /private/tmp/docker_tmp5au7853y\nDEBUG cwltool:job.py:454 [job listing_v1_0.cwl] Removing temporary directory /private/tmp/docker_tmps8sr21xg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp48ro06s9\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7399552670003686, 'start': 1685951432.334913, 'stop': 1685951433.074852, '$report_type': 'TestReport', 'item_index': 367, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_listing_v1_0', 'location': ('tests/test_ext.py', 63, 'test_listing_v1_0'), 'keywords': {'test_listing_v1_0': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl'\n\x1b[1;30mINFO\x1b[0m [job listing_v1_0.cwl] /private/tmp/docker_tmp48ro06s9$ echo \\\n /private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\n/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\n\x1b[1;30mINFO\x1b[0m [job listing_v1_0.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job listing_v1_0.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\nDEBUG cwltool:command_line_tool.py:988 [job listing_v1_0.cwl] {\n "d": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1",\n "basename": "tmp1",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2",\n "basename": "tmp2",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3",\n "basename": "tmp3",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep",\n "basename": ".gitkeep",\n "size": 0\n }\n ]\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job listing_v1_0.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp1/tmp2/tmp3/.gitkeep",\n "/private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3/.gitkeep",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job listing_v1_0.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.d.listing[0].listing[0])"\n }\n]\nDEBUG cwltool:job.py:215 [job listing_v1_0.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job listing_v1_0.cwl] /private/tmp/docker_tmp48ro06s9$ echo \\\n /private/tmp/docker_tmp5au7853y/stg76e899e4-0cac-4aca-9094-122d28eba426/tmp1/tmp2/tmp3\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job listing_v1_0.cwl] completed success\nDEBUG cwltool:job.py:422 [job listing_v1_0.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job listing_v1_0.cwl] Removing input staging directory /private/tmp/docker_tmp5au7853y\nDEBUG cwltool:job.py:454 [job listing_v1_0.cwl] Removing temporary directory /private/tmp/docker_tmps8sr21xg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp48ro06s9\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006402729995897971, 'start': 1685951433.076601, 'stop': 1685951433.0772438, '$report_type': 'TestReport', 'item_index': 367, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_listing_v1_0 - location: ('tests/test_ext.py', 63, 'test_listing_v1_0') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_ext.py::test_listing_v1_1 - location: ('tests/test_ext.py', 69, 'test_listing_v1_1') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_listing_v1_1', 'location': ('tests/test_ext.py', 69, 'test_listing_v1_1'), 'keywords': {'test_listing_v1_1': 1, 'skipif': 1, 'skip': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_ext.py', 70, 'Skipped: This is not the default behaviour yet'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002449390003675944, 'start': 1685951433.07875, 'stop': 1685951433.078996, '$report_type': 'TestReport', 'item_index': 368, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_listing_v1_1', 'location': ('tests/test_ext.py', 69, 'test_listing_v1_1'), 'keywords': {'test_listing_v1_1': 1, 'skipif': 1, 'skip': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00018128899955627276, 'start': 1685951433.079686, 'stop': 1685951433.079869, '$report_type': 'TestReport', 'item_index': 368, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_listing_v1_1 - location: ('tests/test_ext.py', 69, 'test_listing_v1_1') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_ext.py::test_double_overwrite - location: ('tests/test_ext.py', 76, 'test_double_overwrite') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_double_overwrite', 'location': ('tests/test_ext.py', 76, 'test_double_overwrite'), 'keywords': {'test_double_overwrite': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016091850002339925, 'start': 1685951433.08082, 'stop': 1685951433.08243, '$report_type': 'TestReport', 'item_index': 369, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_checklink_outputSource', 'location': ('tests/test_load_tool.py', 52, 'test_checklink_outputSource'), 'keywords': {'test_checklink_outputSource': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "[worker-gw3] received command runtests {'indices': [432, 433, 434, 435, 436, 437, 438, 439]}\n\x1b[32m[2023-06-05 09:50:32]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\n\x1b[32m[2023-06-05 09:50:33]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'")], 'duration': 0.2310436990001108, 'start': 1685951432.901361, 'stop': 1685951433.132401, '$report_type': 'TestReport', 'item_index': 412, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_checklink_outputSource', 'location': ('tests/test_load_tool.py', 52, 'test_checklink_outputSource'), 'keywords': {'test_checklink_outputSource': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "[worker-gw3] received command runtests {'indices': [432, 433, 434, 435, 436, 437, 438, 439]}\n\x1b[32m[2023-06-05 09:50:32]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\n\x1b[32m[2023-06-05 09:50:33]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl'")], 'duration': 0.0003706219995365245, 'start': 1685951433.133274, 'stop': 1685951433.1336472, '$report_type': 'TestReport', 'item_index': 412, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_load_tool.py::test_checklink_outputSource - location: ('tests/test_load_tool.py', 52, 'test_checklink_outputSource') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_load_tool.py::test_load_graph_fragment - location: ('tests/test_load_tool.py', 65, 'test_load_graph_fragment') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment', 'location': ('tests/test_load_tool.py', 65, 'test_load_graph_fragment'), 'keywords': {'test_load_graph_fragment': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003440290001890389, 'start': 1685951433.135226, 'stop': 1685951433.135571, '$report_type': 'TestReport', 'item_index': 413, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment', 'location': ('tests/test_load_tool.py', 65, 'test_load_graph_fragment'), 'keywords': {'test_load_graph_fragment': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.1476936069993826, 'start': 1685951433.1362, 'stop': 1685951433.283893, '$report_type': 'TestReport', 'item_index': 413, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment', 'location': ('tests/test_load_tool.py', 65, 'test_load_graph_fragment'), 'keywords': {'test_load_graph_fragment': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002599459994598874, 'start': 1685951433.284791, 'stop': 1685951433.285053, '$report_type': 'TestReport', 'item_index': 413, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_load_tool.py::test_load_graph_fragment - location: ('tests/test_load_tool.py', 65, 'test_load_graph_fragment') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment_from_packed', 'location': ('tests/test_load_tool.py', 83, 'test_load_graph_fragment_from_packed'), 'keywords': {'test_load_graph_fragment_from_packed': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00026335099937568884, 'start': 1685951433.286043, 'stop': 1685951433.286308, '$report_type': 'TestReport', 'item_index': 414, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_load_tool.py::test_load_graph_fragment_from_packed - location: ('tests/test_load_tool.py', 83, 'test_load_graph_fragment_from_packed') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations', 'location': ('tests/test_iwdr.py', 79, 'test_iwdr_permutations'), 'keywords': {'test_iwdr_permutations': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'failed', 'longrepr': {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 'lineno': 132, 'message': 'assert 1 == 0'}, 'reprtraceback': {'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_iwdr_permutations(tmp_path_factory: Any) -> None:', ' misc = tmp_path_factory.mktemp("misc")', ' fifth = misc / "fifth"', ' fifth.mkdir()', ' sixth = misc / "sixth"', ' sixth.mkdir()', ' seventh = misc / "seventh"', ' seventh.mkdir()', ' eighth = misc / "eighth"', ' eighth.mkdir()', ' first = misc / "first"', ' first.touch()', ' second = misc / "second"', ' second.touch()', ' third = misc / "third"', ' third.touch()', ' fourth = misc / "fourth"', ' fourth.touch()', ' eleventh = misc / "eleventh"', ' eleventh.touch()', ' twelfth = misc / "twelfth"', ' twelfth.touch()', ' outdir = str(tmp_path_factory.mktemp("outdir"))', ' err_code, stdout, _ = get_main_output(', ' [', ' "--outdir",', ' outdir,', ' "--debug",', ' get_data("tests/wf/iwdr_permutations.cwl"),', ' "--first",', ' str(first),', ' "--second",', ' str(second),', ' "--third",', ' str(third),', ' "--fourth",', ' str(fourth),', ' "--fifth",', ' str(fifth),', ' "--sixth",', ' str(sixth),', ' "--seventh",', ' str(seventh),', ' "--eighth",', ' str(eighth),', ' "--eleventh",', ' str(eleventh),', ' "--eleventh",', ' str(twelfth),', ' ]', ' )', '> assert err_code == 0', 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path_factory', "TempPathFactory(_given_basetemp=PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/.../8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4'), _retention_count=3, _retention_policy='all')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_iwdr.py', 'lineno': 132, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, 'sections': [], 'chain': [({'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_iwdr_permutations(tmp_path_factory: Any) -> None:', ' misc = tmp_path_factory.mktemp("misc")', ' fifth = misc / "fifth"', ' fifth.mkdir()', ' sixth = misc / "sixth"', ' sixth.mkdir()', ' seventh = misc / "seventh"', ' seventh.mkdir()', ' eighth = misc / "eighth"', ' eighth.mkdir()', ' first = misc / "first"', ' first.touch()', ' second = misc / "second"', ' second.touch()', ' third = misc / "third"', ' third.touch()', ' fourth = misc / "fourth"', ' fourth.touch()', ' eleventh = misc / "eleventh"', ' eleventh.touch()', ' twelfth = misc / "twelfth"', ' twelfth.touch()', ' outdir = str(tmp_path_factory.mktemp("outdir"))', ' err_code, stdout, _ = get_main_output(', ' [', ' "--outdir",', ' outdir,', ' "--debug",', ' get_data("tests/wf/iwdr_permutations.cwl"),', ' "--first",', ' str(first),', ' "--second",', ' str(second),', ' "--third",', ' str(third),', ' "--fourth",', ' str(fourth),', ' "--fifth",', ' str(fifth),', ' "--sixth",', ' str(sixth),', ' "--seventh",', ' str(seventh),', ' "--eighth",', ' str(eighth),', ' "--eleventh",', ' str(eleventh),', ' "--eleventh",', ' str(twelfth),', ' ]', ' )', '> assert err_code == 0', 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path_factory', "TempPathFactory(_given_basetemp=PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/.../8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4'), _retention_count=3, _retention_policy='all')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_iwdr.py', 'lineno': 132, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, {'path': '/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 'lineno': 132, 'message': 'assert 1 == 0'}, None)]}, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\'\nDEBUG cwltool:main.py:463 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"file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh",\n "/GbFKKR/eleventh",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth",\n "/GbFKKR/twelfth",\n "File",\n true\n ],\n "_:97279cd1-e7c6-4935-80a6-4f84eeccac8f": [\n "baz",\n "/my_path/my_file_literal",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations.cwl] /private/tmp/docker_tmp_w3qy9tv$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_w3qy9tv,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpxys67wcx,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second,target=/GbFKKR/second_read_only_file,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpws1207gg/third,target=/my_path/third_writable_file \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth,target=/my_other_path/fourth_read_only_file,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth,target=/GbFKKR/sixth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmp073wgswq/seventh,target=/my_path/seventh_writable_directory \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth,target=/my_other_path/eighth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpy0u8j74x/tenth_writable_directory_literal,target=/my_path/tenth_writable_directory_literal \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh,target=/GbFKKR/eleventh,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth,target=/GbFKKR/twelfth,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmps1fmotdc/my_file_literal,target=/my_path/my_file_literal,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpgl_ulo2z/20230605095032-664292.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n --env=LC_ALL=C \\\n docker.io/debian:stable-slim \\\n bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\necho "a" > first_writable_file\necho "b" > /my_path/third_writable_file\ntouch fifth_writable_directory/c\ntouch /my_path/seventh_writable_directory/d\nfind . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\n\' > /private/tmp/docker_tmp_w3qy9tv/log.txt\nINFO cwltool:job.py:905 [job iwdr_permutations.cwl] Max memory used: 0MiB\nERROR cwltool:job.py:395 Exception while running job\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 373, in _execute\n relink_initialworkdir(\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 103, in relink_initialworkdir\n shutil.rmtree(host_outdir_tgt)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 731, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 729, in rmtree\n os.rmdir(path)\nPermissionError: [Errno 13] Permission denied: \'/private/tmp/docker_tmp_w3qy9tv/sixth_read_only_directory\'\nWARNING cwltool:job.py:417 [job iwdr_permutations.cwl] completed permanentFail\nDEBUG cwltool:job.py:422 [job iwdr_permutations.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr_permutations.cwl] Removing input staging directory /private/tmp/docker_tmp9bhpnx_4\nDEBUG cwltool:job.py:454 [job iwdr_permutations.cwl] Removing temporary directory /private/tmp/docker_tmpxys67wcx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_w3qy9tv\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 1.8349911279992739, 'start': 1685951431.870146, 'stop': 1685951433.7050948, '$report_type': 'TestReport', 'item_index': 396, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations', 'location': ('tests/test_iwdr.py', 79, 'test_iwdr_permutations'), 'keywords': {'test_iwdr_permutations': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl",\n "eighth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth"\n },\n "eleventh": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth"\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first"\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second"\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth"\n },\n "tenth": {\n "class": "Directory",\n "basename": "bar",\n "listing": []\n },\n "third": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr_permutations.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr_permutations.cwl] {\n "eighth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth",\n "basename": "eighth"\n },\n "eleventh": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh",\n "size": 0,\n "basename": "eleventh",\n "nameroot": "eleventh",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth",\n "size": 0,\n "basename": "twelfth",\n "nameroot": "twelfth",\n "nameext": ""\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth",\n "size": 0,\n "basename": "fourth",\n "nameroot": "fourth",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:631d8639-cc11-4787-9f3d-48b57039c0a6"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh",\n "basename": "seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth",\n "basename": "sixth"\n },\n "tenth": {\n "class": "Directory",\n "basename": "bar",\n "listing": [],\n "location": "_:5cd11e38-0800-4f65-ae18-9082ec81cb93"\n },\n "third": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third",\n "size": 0,\n "basename": "third",\n "nameroot": "third",\n "nameext": ""\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr_permutations.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth",\n "/my_other_path/eighth_read_only_directory",\n "Directory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh",\n "/GbFKKR/eleventh",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth",\n "/GbFKKR/twelfth",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n false\n ],\n "_:631d8639-cc11-4787-9f3d-48b57039c0a6": [\n "_:631d8639-cc11-4787-9f3d-48b57039c0a6",\n 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"_:5cd11e38-0800-4f65-ae18-9082ec81cb93": [\n "_:5cd11e38-0800-4f65-ae18-9082ec81cb93",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third",\n "/my_path/third_writable_file",\n "WritableFile",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr_permutations.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\necho \\"a\\" > first_writable_file\\necho \\"b\\" > /my_path/third_writable_file\\ntouch fifth_writable_directory/c\\ntouch /my_path/seventh_writable_directory/d\\nfind . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\n"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr_permutations.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second",\n "/GbFKKR/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/third",\n "/my_path/third_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth",\n "/GbFKKR/sixth_read_only_directory",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth",\n "/my_other_path/eighth_read_only_directory",\n "Directory",\n true\n ],\n "_:631d8639-cc11-4787-9f3d-48b57039c0a6": [\n "_:631d8639-cc11-4787-9f3d-48b57039c0a6",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "_:5cd11e38-0800-4f65-ae18-9082ec81cb93": [\n "_:5cd11e38-0800-4f65-ae18-9082ec81cb93",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh",\n "/GbFKKR/eleventh",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth",\n "/GbFKKR/twelfth",\n "File",\n true\n ],\n "_:97279cd1-e7c6-4935-80a6-4f84eeccac8f": [\n "baz",\n "/my_path/my_file_literal",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations.cwl] /private/tmp/docker_tmp_w3qy9tv$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_w3qy9tv,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpxys67wcx,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/second,target=/GbFKKR/second_read_only_file,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpws1207gg/third,target=/my_path/third_writable_file \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/fourth,target=/my_other_path/fourth_read_only_file,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/sixth,target=/GbFKKR/sixth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmp073wgswq/seventh,target=/my_path/seventh_writable_directory \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eighth,target=/my_other_path/eighth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpy0u8j74x/tenth_writable_directory_literal,target=/my_path/tenth_writable_directory_literal \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/eleventh,target=/GbFKKR/eleventh,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc0/twelfth,target=/GbFKKR/twelfth,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmps1fmotdc/my_file_literal,target=/my_path/my_file_literal,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpgl_ulo2z/20230605095032-664292.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n --env=LC_ALL=C \\\n docker.io/debian:stable-slim \\\n bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\necho "a" > first_writable_file\necho "b" > /my_path/third_writable_file\ntouch fifth_writable_directory/c\ntouch /my_path/seventh_writable_directory/d\nfind . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\n\' > /private/tmp/docker_tmp_w3qy9tv/log.txt\nINFO cwltool:job.py:905 [job iwdr_permutations.cwl] Max memory used: 0MiB\nERROR cwltool:job.py:395 Exception while running job\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 373, in _execute\n relink_initialworkdir(\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 103, in relink_initialworkdir\n shutil.rmtree(host_outdir_tgt)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 731, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 729, in rmtree\n os.rmdir(path)\nPermissionError: [Errno 13] Permission denied: \'/private/tmp/docker_tmp_w3qy9tv/sixth_read_only_directory\'\nWARNING cwltool:job.py:417 [job iwdr_permutations.cwl] completed permanentFail\nDEBUG cwltool:job.py:422 [job iwdr_permutations.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr_permutations.cwl] Removing input staging directory /private/tmp/docker_tmp9bhpnx_4\nDEBUG cwltool:job.py:454 [job iwdr_permutations.cwl] Removing temporary directory /private/tmp/docker_tmpxys67wcx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_w3qy9tv\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.001088491000700742, 'start': 1685951433.917353, 'stop': 1685951433.918443, '$report_type': 'TestReport', 'item_index': 396, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_iwdr.py::test_iwdr_permutations - location: ('tests/test_iwdr.py', 79, 'test_iwdr_permutations') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_iwdr.py::test_iwdr_permutations_readonly - location: ('tests/test_iwdr.py', 138, 'test_iwdr_permutations_readonly') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_readonly', 'location': ('tests/test_iwdr.py', 138, 'test_iwdr_permutations_readonly'), 'keywords': {'test_iwdr_permutations_readonly': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003601219996198779, 'start': 1685951433.9202828, 'stop': 1685951433.920644, '$report_type': 'TestReport', 'item_index': 397, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment_from_packed', 'location': ('tests/test_load_tool.py', 83, 'test_load_graph_fragment_from_packed'), 'keywords': {'test_load_graph_fragment_from_packed': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.9820490420006536, 'start': 1685951433.286717, 'stop': 1685951434.2687428, '$report_type': 'TestReport', 'item_index': 414, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_graph_fragment_from_packed', 'location': ('tests/test_load_tool.py', 83, 'test_load_graph_fragment_from_packed'), 'keywords': {'test_load_graph_fragment_from_packed': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002711429997361847, 'start': 1685951434.269431, 'stop': 1685951434.2697039, '$report_type': 'TestReport', 'item_index': 414, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_load_tool.py::test_load_graph_fragment_from_packed - location: ('tests/test_load_tool.py', 83, 'test_load_graph_fragment_from_packed') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_load_tool.py::test_import_tracked - location: ('tests/test_load_tool.py', 130, 'test_import_tracked') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_import_tracked', 'location': ('tests/test_load_tool.py', 130, 'test_import_tracked'), 'keywords': {'test_import_tracked': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002453380002407357, 'start': 1685951434.270707, 'stop': 1685951434.270954, '$report_type': 'TestReport', 'item_index': 415, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_readonly', 'location': ('tests/test_iwdr.py', 138, 'test_iwdr_permutations_readonly'), 'keywords': {'test_iwdr_permutations_readonly': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "basename": "sixth_read_only_directory",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/second_read_only_file",\n "basename": "second_read_only_file",\n "path": "/private/tmp/docker_tmpp5625vra/second_read_only_file"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/first_writable_file",\n "basename": "first_writable_file",\n "path": "/private/tmp/docker_tmpp5625vra/first_writable_file"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "basename": "fifth_writable_directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/foo",\n "basename": "foo",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/foo"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/bar",\n "basename": "bar",\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/bar"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/c",\n "basename": "c",\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/c"\n }\n ],\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "basename": "nineth_writable_directory_literal",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal"\n }\n ],\n "path": "/private/tmp/docker_tmpp5625vra"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl",\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] {\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:1f56c615-53c2-403e-b9c7-4924d21f8b70"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "basename": "sixth0"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n false\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\necho \\"a\\" > first_writable_file\\ntouch fifth_writable_directory/c\\n"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n true\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job iwdr_permutations_nocontainer.cwl] /private/tmp/docker_tmpp5625vra$ bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\necho "a" > first_writable_file\ntouch fifth_writable_directory/c\n\'\n.\n./fifth_writable_directory\n./fifth_writable_directory/bar\n./fifth_writable_directory/foo\n./first_writable_file\n./nineth_writable_directory_literal\n./second_read_only_file\n./sixth_read_only_directory\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job iwdr_permutations_nocontainer.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "nameroot": "docker_tmpp5625vra",\n "nameext": "",\n "class": "Directory"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] Removing input staging directory /private/tmp/docker_tmpjhjm2onk\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] Removing temporary directory /private/tmp/docker_tmpk21vv0i5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpp5625vra\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl",\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr_permutations_nocontainer.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr_permutations_nocontainer.cwl] {\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:1f56c615-53c2-403e-b9c7-4924d21f8b70"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "basename": "sixth0"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr_permutations_nocontainer.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n false\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr_permutations_nocontainer.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\necho \\"a\\" > first_writable_file\\ntouch fifth_writable_directory/c\\n"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr_permutations_nocontainer.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n true\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations_nocontainer.cwl] /private/tmp/docker_tmpp5625vra$ bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\necho "a" > first_writable_file\ntouch fifth_writable_directory/c\n\'\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr_permutations_nocontainer.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr_permutations_nocontainer.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "nameroot": "docker_tmpp5625vra",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job iwdr_permutations_nocontainer.cwl] Removing input staging directory /private/tmp/docker_tmpjhjm2onk\nDEBUG cwltool:job.py:454 [job iwdr_permutations_nocontainer.cwl] Removing temporary directory /private/tmp/docker_tmpk21vv0i5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp5625vra\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.8987138219999906, 'start': 1685951433.9209988, 'stop': 1685951434.819693, '$report_type': 'TestReport', 'item_index': 397, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_readonly', 'location': ('tests/test_iwdr.py', 138, 'test_iwdr_permutations_readonly'), 'keywords': {'test_iwdr_permutations_readonly': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "basename": "sixth_read_only_directory",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/second_read_only_file",\n "basename": "second_read_only_file",\n "path": "/private/tmp/docker_tmpp5625vra/second_read_only_file"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/first_writable_file",\n "basename": "first_writable_file",\n "path": "/private/tmp/docker_tmpp5625vra/first_writable_file"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "basename": "fifth_writable_directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/foo",\n "basename": "foo",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/foo"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/bar",\n "basename": "bar",\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/bar"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpp5625vra/fifth_writable_directory/c",\n "basename": "c",\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory/c"\n }\n ],\n "path": "/private/tmp/docker_tmpp5625vra/fifth_writable_directory"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "basename": "nineth_writable_directory_literal",\n "listing": [],\n "path": "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal"\n }\n ],\n "path": "/private/tmp/docker_tmpp5625vra"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl",\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] {\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:1f56c615-53c2-403e-b9c7-4924d21f8b70"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "basename": "sixth0"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n false\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\necho \\"a\\" > first_writable_file\\ntouch fifth_writable_directory/c\\n"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n true\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job iwdr_permutations_nocontainer.cwl] /private/tmp/docker_tmpp5625vra$ bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\necho "a" > first_writable_file\ntouch fifth_writable_directory/c\n\'\n.\n./fifth_writable_directory\n./fifth_writable_directory/bar\n./fifth_writable_directory/foo\n./first_writable_file\n./nineth_writable_directory_literal\n./second_read_only_file\n./sixth_read_only_directory\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job iwdr_permutations_nocontainer.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "nameroot": "docker_tmpp5625vra",\n "nameext": "",\n "class": "Directory"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] Removing input staging directory /private/tmp/docker_tmpjhjm2onk\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr_permutations_nocontainer.cwl] Removing temporary directory /private/tmp/docker_tmpk21vv0i5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpp5625vra\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl",\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr_permutations_nocontainer.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations_nocontainer.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr_permutations_nocontainer.cwl] {\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:1f56c615-53c2-403e-b9c7-4924d21f8b70"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "basename": "sixth0"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr_permutations_nocontainer.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n false\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr_permutations_nocontainer.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\necho \\"a\\" > first_writable_file\\ntouch fifth_writable_directory/c\\n"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr_permutations_nocontainer.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/first",\n "/private/tmp/docker_tmpp5625vra/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/second",\n "/private/tmp/docker_tmpp5625vra/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc1/fifth",\n "/private/tmp/docker_tmpp5625vra/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/sixth0",\n "/private/tmp/docker_tmpp5625vra/sixth_read_only_directory",\n "Directory",\n true\n ],\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70": [\n "_:1f56c615-53c2-403e-b9c7-4924d21f8b70",\n "/private/tmp/docker_tmpp5625vra/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations_nocontainer.cwl] /private/tmp/docker_tmpp5625vra$ bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\necho "a" > first_writable_file\ntouch fifth_writable_directory/c\n\'\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr_permutations_nocontainer.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr_permutations_nocontainer.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpp5625vra",\n "basename": "docker_tmpp5625vra",\n "nameroot": "docker_tmpp5625vra",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job iwdr_permutations_nocontainer.cwl] Removing input staging directory /private/tmp/docker_tmpjhjm2onk\nDEBUG cwltool:job.py:454 [job iwdr_permutations_nocontainer.cwl] Removing temporary directory /private/tmp/docker_tmpk21vv0i5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp5625vra\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00042286200005037244, 'start': 1685951434.821234, 'stop': 1685951434.8216588, '$report_type': 'TestReport', 'item_index': 397, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_iwdr.py::test_iwdr_permutations_readonly - location: ('tests/test_iwdr.py', 138, 'test_iwdr_permutations_readonly') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_inplace', 'location': ('tests/test_iwdr.py', 188, 'test_iwdr_permutations_inplace'), 'keywords': {'test_iwdr_permutations_inplace': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005866809997314704, 'start': 1685951434.8234959, 'stop': 1685951434.824085, '$report_type': 'TestReport', 'item_index': 398, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_iwdr.py::test_iwdr_permutations_inplace - location: ('tests/test_iwdr.py', 188, 'test_iwdr_permutations_inplace') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[]'), 'keywords': {'test_cache_relative_paths[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmpu4gvxfws/stg543c1c83-2e8e-49d1-86fa-ec758f66c2ba/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmpu4gvxfws/stg543c1c83-2e8e-49d1-86fa-ec758f66c2ba/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job secondary-files.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl] Removing input staging directory /private/tmp/docker_tmpu4gvxfws\nDEBUG cwltool:job.py:454 [job secondary-files.cwl] Removing temporary directory /private/tmp/docker_tmpk1mp264l\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cacheckg89j70\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_2] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_2] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cachee9f67smd\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.106250634999924, 'start': 1685951432.897739, 'stop': 1685951435.003938, '$report_type': 'TestReport', 'item_index': 300, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[]'), 'keywords': {'test_cache_relative_paths[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmpu4gvxfws/stg543c1c83-2e8e-49d1-86fa-ec758f66c2ba/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmpu4gvxfws/stg543c1c83-2e8e-49d1-86fa-ec758f66c2ba/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job secondary-files.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl] Removing input staging directory /private/tmp/docker_tmpu4gvxfws\nDEBUG cwltool:job.py:454 [job secondary-files.cwl] Removing temporary directory /private/tmp/docker_tmpk1mp264l\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cacheckg89j70\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_2] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_2] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths__0/cwltool_cachee9f67smd\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005469789994094754, 'start': 1685951435.004695, 'stop': 1685951435.0052428, '$report_type': 'TestReport', 'item_index': 300, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cache_relative_paths[] - location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cache_relative_paths[--parallel] - location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel]'), 'keywords': {'test_cache_relative_paths[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0020195979996060487, 'start': 1685951435.007218, 'stop': 1685951435.0092402, '$report_type': 'TestReport', 'item_index': 301, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_import_tracked', 'location': ('tests/test_load_tool.py', 130, 'test_import_tracked'), 'keywords': {'test_import_tracked': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:34]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl'\n\x1b[32m[2023-06-05 09:50:35]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811.cwl'")], 'duration': 1.5744697370000722, 'start': 1685951434.271424, 'stop': 1685951435.845856, '$report_type': 'TestReport', 'item_index': 415, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_import_tracked', 'location': ('tests/test_load_tool.py', 130, 'test_import_tracked'), 'keywords': {'test_import_tracked': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:34]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl'\n\x1b[32m[2023-06-05 09:50:35]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811-12.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/811.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/811.cwl'")], 'duration': 0.00018237499989481876, 'start': 1685951435.846292, 'stop': 1685951435.8464751, '$report_type': 'TestReport', 'item_index': 415, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_load_tool.py::test_import_tracked - location: ('tests/test_load_tool.py', 130, 'test_import_tracked') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_load_tool.py::test_load_badhints - location: ('tests/test_load_tool.py', 148, 'test_load_badhints') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints', 'location': ('tests/test_load_tool.py', 148, 'test_load_badhints'), 'keywords': {'test_load_badhints': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00018566800008557038, 'start': 1685951435.8474848, 'stop': 1685951435.847672, '$report_type': 'TestReport', 'item_index': 416, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints', 'location': ('tests/test_load_tool.py', 148, 'test_load_badhints'), 'keywords': {'test_load_badhints': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.02006813099978899, 'start': 1685951435.847969, 'stop': 1685951435.868038, '$report_type': 'TestReport', 'item_index': 416, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints', 'location': ('tests/test_load_tool.py', 148, 'test_load_badhints'), 'keywords': {'test_load_badhints': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00018017899947153637, 'start': 1685951435.868441, 'stop': 1685951435.868622, '$report_type': 'TestReport', 'item_index': 416, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_load_tool.py::test_load_badhints - location: ('tests/test_load_tool.py', 148, 'test_load_badhints') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_load_tool.py::test_load_badhints_nodict - location: ('tests/test_load_tool.py', 159, 'test_load_badhints_nodict') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints_nodict', 'location': ('tests/test_load_tool.py', 159, 'test_load_badhints_nodict'), 'keywords': {'test_load_badhints_nodict': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0001881380003396771, 'start': 1685951435.869579, 'stop': 1685951435.869768, '$report_type': 'TestReport', 'item_index': 417, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints_nodict', 'location': ('tests/test_load_tool.py', 159, 'test_load_badhints_nodict'), 'keywords': {'test_load_badhints_nodict': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.019618063000052643, 'start': 1685951435.870068, 'stop': 1685951435.889687, '$report_type': 'TestReport', 'item_index': 417, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_load_tool.py::test_load_badhints_nodict', 'location': ('tests/test_load_tool.py', 159, 'test_load_badhints_nodict'), 'keywords': {'test_load_badhints_nodict': 1, 'test_load_tool.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00021258099968690658, 'start': 1685951435.8901, 'stop': 1685951435.890314, '$report_type': 'TestReport', 'item_index': 417, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_load_tool.py::test_load_badhints_nodict - location: ('tests/test_load_tool.py', 159, 'test_load_badhints_nodict') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_loop_with_all_output_method - location: ('tests/test_loop.py', 161, 'test_loop_with_all_output_method') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method', 'location': ('tests/test_loop.py', 161, 'test_loop_with_all_output_method'), 'keywords': {'test_loop_with_all_output_method': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002493149995643762, 'start': 1685951435.891244, 'stop': 1685951435.8914938, '$report_type': 'TestReport', 'item_index': 432, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_dir[--debug]', 'location': ('tests/test_examples.py', 1084, 'test_cid_file_dir[--debug]'), 'keywords': {'test_cid_file_dir[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_3\nDEBUG cwltool:workflow_job.py:727 [step task2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_3] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_3\nDEBUG cwltool:command_line_tool.py:988 [job task2_3] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_3] initial work dir {}\nINFO cwltool:job.py:266 [job task2_3] /private/tmp/docker_tmp1nnhk1t7$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp1nnhk1t7,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmpod5r_84n,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_cid_file_dir___debug_0/20230605095034-025713.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_3] completed success\nDEBUG cwltool:job.py:422 [job task2_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1nnhk1t7/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_3] completed success\nDEBUG cwltool:job.py:446 [job task2_3] Removing input staging directory /private/tmp/docker_tmpwq9_h_7z\nDEBUG cwltool:job.py:454 [job task2_3] Removing temporary directory /private/tmp/docker_tmpod5r_84n\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_3\nDEBUG cwltool:workflow_job.py:727 [step task1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_3\nDEBUG cwltool:command_line_tool.py:988 [job task1_3] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_3] initial work dir {}\nINFO cwltool:job.py:266 [job task1_3] /private/tmp/docker_tmpudmds_on$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpudmds_on,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmpa5phkv0m,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_cid_file_dir___debug_0/20230605095035-063346.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_3] completed success\nDEBUG cwltool:job.py:422 [job task1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpudmds_on/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_3] Removing input staging directory /private/tmp/docker_tmp_be0w_8a\nDEBUG cwltool:job.py:454 [job task1_3] Removing temporary directory /private/tmp/docker_tmpa5phkv0m\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1nnhk1t7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpudmds_on\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwhodp045\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 3.749131440000383, 'start': 1685951432.337434, 'stop': 1685951436.086473, '$report_type': 'TestReport', 'item_index': 266, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_dir[--debug]', 'location': ('tests/test_examples.py', 1084, 'test_cid_file_dir[--debug]'), 'keywords': {'test_cid_file_dir[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_3\nDEBUG cwltool:workflow_job.py:727 [step task2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_3] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_3\nDEBUG cwltool:command_line_tool.py:988 [job task2_3] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_3] initial work dir {}\nINFO cwltool:job.py:266 [job task2_3] /private/tmp/docker_tmp1nnhk1t7$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp1nnhk1t7,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmpod5r_84n,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_cid_file_dir___debug_0/20230605095034-025713.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_3] completed success\nDEBUG cwltool:job.py:422 [job task2_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1nnhk1t7/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_3] completed success\nDEBUG cwltool:job.py:446 [job task2_3] Removing input staging directory /private/tmp/docker_tmpwq9_h_7z\nDEBUG cwltool:job.py:454 [job task2_3] Removing temporary directory /private/tmp/docker_tmpod5r_84n\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_3\nDEBUG cwltool:workflow_job.py:727 [step task1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_3\nDEBUG cwltool:command_line_tool.py:988 [job task1_3] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_3] initial work dir {}\nINFO cwltool:job.py:266 [job task1_3] /private/tmp/docker_tmpudmds_on$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpudmds_on,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmpa5phkv0m,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_cid_file_dir___debug_0/20230605095035-063346.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_3] completed success\nDEBUG cwltool:job.py:422 [job task1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpudmds_on/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_3] Removing input staging directory /private/tmp/docker_tmp_be0w_8a\nDEBUG cwltool:job.py:454 [job task1_3] Removing temporary directory /private/tmp/docker_tmpa5phkv0m\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1nnhk1t7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpudmds_on\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwhodp045\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005957659996056464, 'start': 1685951436.0874019, 'stop': 1685951436.0879989, '$report_type': 'TestReport', 'item_index': 266, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_dir[--debug] - location: ('tests/test_examples.py', 1084, 'test_cid_file_dir[--debug]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_validate_loop - location: ('tests/test_loop.py', 10, 'test_validate_loop') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop', 'location': ('tests/test_loop.py', 10, 'test_validate_loop'), 'keywords': {'test_validate_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00019735000023501925, 'start': 1685951436.0892, 'stop': 1685951436.089399, '$report_type': 'TestReport', 'item_index': 418, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method', 'location': ('tests/test_loop.py', 161, 'test_loop_with_all_output_method'), 'keywords': {'test_loop_with_all_output_method': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/all-output-loop.cwl:25:7: object id 'tests/loop/all-output-loop.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _6] start\n\x1b[1;30mINFO\x1b[0m [workflow _6] starting step subworkflow\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _6] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/all-output-loop.cwl:25:7: object id \'tests/loop/all-output-loop.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _6] start\nDEBUG cwltool:workflow_job.py:777 [workflow _6] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _6] starting step subworkflow\nDEBUG cwltool:workflow_job.py:727 [step subworkflow] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow] inputs was {\n "i1": 10\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": [\n 2,\n 3,\n 4,\n 5,\n 6,\n 7,\n 8,\n 9,\n 10\n ]\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow] completed success\nINFO cwltool:workflow_job.py:539 [workflow _6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _6] outputs {\n "o1": [\n 2,\n 3,\n 4,\n 5,\n 6,\n 7,\n 8,\n 9,\n 10\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptip_9h3h\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.8467874959997062, 'start': 1685951435.892153, 'stop': 1685951436.738921, '$report_type': 'TestReport', 'item_index': 432, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method', 'location': ('tests/test_loop.py', 161, 'test_loop_with_all_output_method'), 'keywords': {'test_loop_with_all_output_method': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/all-output-loop.cwl:25:7: object id 'tests/loop/all-output-loop.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _6] start\n\x1b[1;30mINFO\x1b[0m [workflow _6] starting step subworkflow\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _6] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/all-output-loop.cwl:25:7: object id \'tests/loop/all-output-loop.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _6] start\nDEBUG cwltool:workflow_job.py:777 [workflow _6] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _6] starting step subworkflow\nDEBUG cwltool:workflow_job.py:727 [step subworkflow] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow] inputs was {\n "i1": 10\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop.cwl#subworkflow/o1": [\n 2,\n 3,\n 4,\n 5,\n 6,\n 7,\n 8,\n 9,\n 10\n ]\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow] completed success\nINFO cwltool:workflow_job.py:539 [workflow _6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _6] outputs {\n "o1": [\n 2,\n 3,\n 4,\n 5,\n 6,\n 7,\n 8,\n 9,\n 10\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptip_9h3h\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0003319159995953669, 'start': 1685951436.7396128, 'stop': 1685951436.739947, '$report_type': 'TestReport', 'item_index': 432, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_loop_with_all_output_method - location: ('tests/test_loop.py', 161, 'test_loop_with_all_output_method') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_loop_with_all_output_method_no_iteration - location: ('tests/test_loop.py', 174, 'test_loop_with_all_output_method_no_iteration') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method_no_iteration', 'location': ('tests/test_loop.py', 174, 'test_loop_with_all_output_method_no_iteration'), 'keywords': {'test_loop_with_all_output_method_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002555680002842564, 'start': 1685951436.74208, 'stop': 1685951436.742337, '$report_type': 'TestReport', 'item_index': 433, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel]'), 'keywords': {'test_cache_relative_paths[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_3] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_3] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_3] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_3] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmpbsfowjeo/stg9c3282a7-e9fe-48f9-b429-4885d74af651/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmpbsfowjeo/stg9c3282a7-e9fe-48f9-b429-4885d74af651/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(secondary-files.cwl_3), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job secondary-files.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_3] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_3] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_3] Removing input staging directory /private/tmp/docker_tmpbsfowjeo\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_3] Removing temporary directory /private/tmp/docker_tmpxeztwk4m\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache483lpwnx\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_4] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_4] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cacheyc1ic0v7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.8110991969997485, 'start': 1685951435.009705, 'stop': 1685951436.8207622, '$report_type': 'TestReport', 'item_index': 301, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel]'), 'keywords': {'test_cache_relative_paths[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_3] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_3] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_3] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_3] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmpbsfowjeo/stg9c3282a7-e9fe-48f9-b429-4885d74af651/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmpbsfowjeo/stg9c3282a7-e9fe-48f9-b429-4885d74af651/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(secondary-files.cwl_3), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job secondary-files.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_3] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_3] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_3] Removing input staging directory /private/tmp/docker_tmpbsfowjeo\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_3] Removing temporary directory /private/tmp/docker_tmpxeztwk4m\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache483lpwnx\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_4] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_4] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cacheyc1ic0v7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007077919999574078, 'start': 1685951436.821831, 'stop': 1685951436.82254, '$report_type': 'TestReport', 'item_index': 301, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cache_relative_paths[--parallel] - location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cache_relative_paths[--debug] - location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--debug]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--debug]'), 'keywords': {'test_cache_relative_paths[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016138500004672096, 'start': 1685951436.824117, 'stop': 1685951436.8257332, '$report_type': 'TestReport', 'item_index': 302, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_require_prefix_timelimit', 'location': ('tests/test_ext.py', 258, 'test_require_prefix_timelimit'), 'keywords': {'test_require_prefix_timelimit': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl'\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] /private/tmp/docker_tmp58pbn2k5$ sleep \\\n 3\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] Max memory used: 1MiB\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/timelimit.cwl:12:1: checking field 'requirements'\ntests/wf/timelimit.cwl:13:3: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#TimeLimit'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl'\n\x1b[1;30mINFO\x1b[0m [job timelimit-fail.cwl] /private/tmp/docker_tmpn6zcewj2$ sleep \\\n 5\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] exceeded time limit of 3 seconds and will be terminated\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job timelimit-fail.cwl] Max memory used: 1MiB\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] was terminated by signal: SIGTERM\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] completed permanentFail\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl",\n "sleep_time": 3\n}\nDEBUG cwltool:command_line_tool.py:982 [job timelimit.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\nDEBUG cwltool:command_line_tool.py:988 [job timelimit.cwl] {\n "sleep_time": 3\n}\nDEBUG cwltool:command_line_tool.py:1000 [job timelimit.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job timelimit.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sleep"\n },\n {\n "position": [\n 0,\n "sleep_time"\n ],\n "datum": 3\n }\n]\nDEBUG cwltool:job.py:215 [job timelimit.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job timelimit.cwl] /private/tmp/docker_tmp58pbn2k5$ sleep \\\n 3\nINFO cwltool:job.py:532 [job timelimit.cwl] Max memory used: 1MiB\nINFO cwltool:job.py:419 [job timelimit.cwl] completed success\nDEBUG cwltool:job.py:422 [job timelimit.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job timelimit.cwl] Removing input staging directory /private/tmp/docker_tmpettflfps\nDEBUG cwltool:job.py:454 [job timelimit.cwl] Removing temporary directory /private/tmp/docker_tmpfantbkdr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp58pbn2k5\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/timelimit.cwl:12:1: checking field \'requirements\'\ntests/wf/timelimit.cwl:13:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#TimeLimit\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job timelimit-fail.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\nDEBUG cwltool:command_line_tool.py:988 [job timelimit-fail.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job timelimit-fail.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job timelimit-fail.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sleep"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "5"\n }\n]\nDEBUG cwltool:job.py:215 [job timelimit-fail.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job timelimit-fail.cwl] /private/tmp/docker_tmpn6zcewj2$ sleep \\\n 5\nWARNING cwltool:job.py:967 [job timelimit-fail.cwl] exceeded time limit of 3 seconds and will be terminated\nINFO cwltool:job.py:532 [job timelimit-fail.cwl] Max memory used: 1MiB\nWARNING cwltool:job.py:363 [job timelimit-fail.cwl] was terminated by signal: SIGTERM\nWARNING cwltool:job.py:417 [job timelimit-fail.cwl] completed permanentFail\nDEBUG cwltool:job.py:422 [job timelimit-fail.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job timelimit-fail.cwl] Removing input staging directory /private/tmp/docker_tmpt1wowho0\nDEBUG cwltool:job.py:454 [job timelimit-fail.cwl] Removing temporary directory /private/tmp/docker_tmp8knp65by\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpn6zcewj2\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 8.512694676000137, 'start': 1685951428.474015, 'stop': 1685951436.986499, '$report_type': 'TestReport', 'item_index': 378, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_require_prefix_timelimit', 'location': ('tests/test_ext.py', 258, 'test_require_prefix_timelimit'), 'keywords': {'test_require_prefix_timelimit': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl'\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] /private/tmp/docker_tmp58pbn2k5$ sleep \\\n 3\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] Max memory used: 1MiB\n\x1b[1;30mINFO\x1b[0m [job timelimit.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/timelimit.cwl:12:1: checking field 'requirements'\ntests/wf/timelimit.cwl:13:3: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#TimeLimit'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl'\n\x1b[1;30mINFO\x1b[0m [job timelimit-fail.cwl] /private/tmp/docker_tmpn6zcewj2$ sleep \\\n 5\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] exceeded time limit of 3 seconds and will be terminated\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job timelimit-fail.cwl] Max memory used: 1MiB\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] was terminated by signal: SIGTERM\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job timelimit-fail.cwl] completed permanentFail\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl",\n "sleep_time": 3\n}\nDEBUG cwltool:command_line_tool.py:982 [job timelimit.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\nDEBUG cwltool:command_line_tool.py:988 [job timelimit.cwl] {\n "sleep_time": 3\n}\nDEBUG cwltool:command_line_tool.py:1000 [job timelimit.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job timelimit.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sleep"\n },\n {\n "position": [\n 0,\n "sleep_time"\n ],\n "datum": 3\n }\n]\nDEBUG cwltool:job.py:215 [job timelimit.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job timelimit.cwl] /private/tmp/docker_tmp58pbn2k5$ sleep \\\n 3\nINFO cwltool:job.py:532 [job timelimit.cwl] Max memory used: 1MiB\nINFO cwltool:job.py:419 [job timelimit.cwl] completed success\nDEBUG cwltool:job.py:422 [job timelimit.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job timelimit.cwl] Removing input staging directory /private/tmp/docker_tmpettflfps\nDEBUG cwltool:job.py:454 [job timelimit.cwl] Removing temporary directory /private/tmp/docker_tmpfantbkdr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp58pbn2k5\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/timelimit.cwl:12:1: checking field \'requirements\'\ntests/wf/timelimit.cwl:13:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#TimeLimit\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job timelimit-fail.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/timelimit-fail.cwl\nDEBUG cwltool:command_line_tool.py:988 [job timelimit-fail.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job timelimit-fail.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job timelimit-fail.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sleep"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "5"\n }\n]\nDEBUG cwltool:job.py:215 [job timelimit-fail.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job timelimit-fail.cwl] /private/tmp/docker_tmpn6zcewj2$ sleep \\\n 5\nWARNING cwltool:job.py:967 [job timelimit-fail.cwl] exceeded time limit of 3 seconds and will be terminated\nINFO cwltool:job.py:532 [job timelimit-fail.cwl] Max memory used: 1MiB\nWARNING cwltool:job.py:363 [job timelimit-fail.cwl] was terminated by signal: SIGTERM\nWARNING cwltool:job.py:417 [job timelimit-fail.cwl] completed permanentFail\nDEBUG cwltool:job.py:422 [job timelimit-fail.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job timelimit-fail.cwl] Removing input staging directory /private/tmp/docker_tmpt1wowho0\nDEBUG cwltool:job.py:454 [job timelimit-fail.cwl] Removing temporary directory /private/tmp/docker_tmp8knp65by\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpn6zcewj2\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.000628123000751657, 'start': 1685951436.9878762, 'stop': 1685951436.988506, '$report_type': 'TestReport', 'item_index': 378, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_require_prefix_timelimit - location: ('tests/test_ext.py', 258, 'test_require_prefix_timelimit') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_ext.py::test_warn_large_inputs - location: ('tests/test_ext.py', 264, 'test_warn_large_inputs') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_warn_large_inputs', 'location': ('tests/test_ext.py', 264, 'test_warn_large_inputs'), 'keywords': {'test_warn_large_inputs': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00031238300016411813, 'start': 1685951436.9900942, 'stop': 1685951436.990408, '$report_type': 'TestReport', 'item_index': 379, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop', 'location': ('tests/test_loop.py', 10, 'test_validate_loop'), 'keywords': {'test_validate_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined")], 'duration': 0.9011028020004233, 'start': 1685951436.089872, 'stop': 1685951436.990954, '$report_type': 'TestReport', 'item_index': 418, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop', 'location': ('tests/test_loop.py', 10, 'test_validate_loop'), 'keywords': {'test_validate_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined")], 'duration': 0.000282838999737578, 'start': 1685951436.9915211, 'stop': 1685951436.9918048, '$report_type': 'TestReport', 'item_index': 418, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_validate_loop - location: ('tests/test_loop.py', 10, 'test_validate_loop') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_validate_loop_fail_no_ext - location: ('tests/test_loop.py', 20, 'test_validate_loop_fail_no_ext') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_no_ext', 'location': ('tests/test_loop.py', 20, 'test_validate_loop_fail_no_ext'), 'keywords': {'test_validate_loop_fail_no_ext': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00032370300050388323, 'start': 1685951436.993045, 'stop': 1685951436.9933708, '$report_type': 'TestReport', 'item_index': 419, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug]', 'location': ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]'), 'keywords': {'test_cid_file_non_existing_dir[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task2_9\nDEBUG cwltool:workflow_job.py:727 [step task2_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_9\nDEBUG cwltool:command_line_tool.py:988 [job task2_7] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_7), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task1_9\nDEBUG cwltool:workflow_job.py:727 [step task1_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_9\nDEBUG cwltool:command_line_tool.py:988 [job task1_7] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_7), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_7] initial work dir {}\nDEBUG cwltool:job.py:215 [job task1_7] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:executors.py:430 Workflow cannot make any more progress.\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcznvku2h\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwnjg_83y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa2g7ccv0\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 4.7696697329993185, 'start': 1685951432.718051, 'stop': 1685951437.487604, '$report_type': 'TestReport', 'item_index': 275, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug]', 'location': ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]'), 'keywords': {'test_cid_file_non_existing_dir[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task2_9\nDEBUG cwltool:workflow_job.py:727 [step task2_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_9\nDEBUG cwltool:command_line_tool.py:988 [job task2_7] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_7), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _9] starting step task1_9\nDEBUG cwltool:workflow_job.py:727 [step task1_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_9] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_9\nDEBUG cwltool:command_line_tool.py:988 [job task1_7] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_7), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_7] initial work dir {}\nDEBUG cwltool:job.py:215 [job task1_7] initial work dir {}\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:docker.py:392 --cidfile-dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_non_existing_dir3/cidfile-dir-badpath error:\ndirectory doesn\'t exist, please create it first\nERROR cwltool:task_queue.py:59 Unhandled exception running task\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/task_queue.py", line 57, in _task_queue_func\n task()\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 314, in _runner\n job.run(runtime_context, TMPDIR_LOCK)\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 827, in run\n (runtime, cidfile) = self.create_runtime(env, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/docker.py", line 397, in create_runtime\n exit(2)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/_sitebuiltins.py", line 26, in __call__\n raise SystemExit(code)\nSystemExit: 2\nERROR cwltool:executors.py:430 Workflow cannot make any more progress.\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcznvku2h\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwnjg_83y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa2g7ccv0\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.0010064870002679527, 'start': 1685951437.488749, 'stop': 1685951437.4897568, '$report_type': 'TestReport', 'item_index': 275, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_non_existing_dir[--parallel --debug] - location: ('tests/test_examples.py', 1116, 'test_cid_file_non_existing_dir[--parallel --debug]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]'), 'keywords': {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016974030004348606, 'start': 1685951437.491211, 'stop': 1685951437.4929101, '$report_type': 'TestReport', 'item_index': 276, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_inplace', 'location': ('tests/test_iwdr.py', 188, 'test_iwdr_permutations_inplace'), 'keywords': {'test_iwdr_permutations_inplace': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'failed', 'longrepr': {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 'lineno': 243, 'message': 'assert 1 == 0'}, 'reprtraceback': {'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_iwdr_permutations_inplace(tmp_path_factory: Any) -> None:', ' misc = tmp_path_factory.mktemp("misc")', ' fifth = misc / "fifth"', ' fifth.mkdir()', ' sixth = misc / "sixth"', ' sixth.mkdir()', ' seventh = misc / "seventh"', ' seventh.mkdir()', ' eighth = misc / "eighth"', ' eighth.mkdir()', ' first = misc / "first"', ' first.touch()', ' second = misc / "second"', ' second.touch()', ' third = misc / "third"', ' third.touch()', ' fourth = misc / "fourth"', ' fourth.touch()', ' eleventh = misc / "eleventh"', ' eleventh.touch()', ' twelfth = misc / "twelfth"', ' twelfth.touch()', ' outdir = str(tmp_path_factory.mktemp("outdir"))', ' err_code, stdout, _ = get_main_output(', ' [', ' "--outdir",', ' outdir,', ' "--enable-ext",', ' "--overrides",', ' get_data("tests/wf/iwdr_permutations_inplace.yml"),', ' get_data("tests/wf/iwdr_permutations.cwl"),', ' "--first",', ' str(first),', ' "--second",', ' str(second),', ' "--third",', ' str(third),', ' "--fourth",', ' str(fourth),', ' "--fifth",', ' str(fifth),', ' "--sixth",', ' str(sixth),', ' "--seventh",', ' str(seventh),', ' "--eighth",', ' str(eighth),', ' "--eleventh",', ' str(eleventh),', ' "--eleventh",', ' str(twelfth),', ' ]', ' )', '> assert err_code == 0', 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path_factory', "TempPathFactory(_given_basetemp=PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/.../8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4'), _retention_count=3, _retention_policy='all')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_iwdr.py', 'lineno': 243, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, 'sections': [], 'chain': [({'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_iwdr_permutations_inplace(tmp_path_factory: Any) -> None:', ' misc = tmp_path_factory.mktemp("misc")', ' fifth = misc / "fifth"', ' fifth.mkdir()', ' sixth = misc / "sixth"', ' sixth.mkdir()', ' seventh = misc / "seventh"', ' seventh.mkdir()', ' eighth = misc / "eighth"', ' eighth.mkdir()', ' first = misc / "first"', ' first.touch()', ' second = misc / "second"', ' second.touch()', ' third = misc / "third"', ' third.touch()', ' fourth = misc / "fourth"', ' fourth.touch()', ' eleventh = misc / "eleventh"', ' eleventh.touch()', ' twelfth = misc / "twelfth"', ' twelfth.touch()', ' outdir = str(tmp_path_factory.mktemp("outdir"))', ' err_code, stdout, _ = get_main_output(', ' [', ' "--outdir",', ' outdir,', ' "--enable-ext",', ' "--overrides",', ' get_data("tests/wf/iwdr_permutations_inplace.yml"),', ' get_data("tests/wf/iwdr_permutations.cwl"),', ' "--first",', ' str(first),', ' "--second",', ' str(second),', ' "--third",', ' str(third),', ' "--fourth",', ' str(fourth),', ' "--fifth",', ' str(fifth),', ' "--sixth",', ' str(sixth),', ' "--seventh",', ' str(seventh),', ' "--eighth",', ' str(eighth),', ' "--eleventh",', ' str(eleventh),', ' "--eleventh",', ' str(twelfth),', ' ]', ' )', '> assert err_code == 0', 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path_factory', "TempPathFactory(_given_basetemp=PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/.../8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4'), _retention_count=3, _retention_policy='all')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_iwdr.py', 'lineno': 243, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, {'path': '/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 'lineno': 243, 'message': 'assert 1 == 0'}, None)]}, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl",\n "eighth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth"\n },\n "eleventh": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth"\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first"\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second"\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": 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"eleventh",\n "nameroot": "eleventh",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "size": 0,\n "basename": "twelfth",\n "nameroot": "twelfth",\n "nameext": ""\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "size": 0,\n "basename": "fourth",\n "nameroot": "fourth",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:0b3439f5-e916-4bb0-875b-01251ced359b"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "basename": "seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "basename": "sixth"\n },\n "tenth": {\n "class": "Directory",\n "basename": "bar",\n "listing": [],\n "location": "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b"\n },\n "third": {\n "class": "File",\n "location": 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"file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "/GbFKKR/twelfth",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n false\n ],\n "_:0b3439f5-e916-4bb0-875b-01251ced359b": [\n "_:0b3439f5-e916-4bb0-875b-01251ced359b",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "/GbFKKR/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "/GbFKKR/sixth_read_only_directory",\n "Directory",\n false\n ],\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b": [\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third",\n "/my_path/third_writable_file",\n "WritableFile",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr_permutations.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\necho \\"a\\" > first_writable_file\\necho \\"b\\" > /my_path/third_writable_file\\ntouch fifth_writable_directory/c\\ntouch /my_path/seventh_writable_directory/d\\nfind . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\n"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr_permutations.cwl_2] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "/GbFKKR/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third",\n "/my_path/third_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "/GbFKKR/sixth_read_only_directory",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth",\n "/my_other_path/eighth_read_only_directory",\n "Directory",\n true\n ],\n "_:0b3439f5-e916-4bb0-875b-01251ced359b": [\n "_:0b3439f5-e916-4bb0-875b-01251ced359b",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b": [\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh",\n "/GbFKKR/eleventh",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "/GbFKKR/twelfth",\n "File",\n true\n ],\n "_:b05fb645-e5b4-4261-ac08-84f2dbf2f4d6": [\n "baz",\n "/my_path/my_file_literal",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations.cwl_2] /private/tmp/docker_tmpcuw6t_2m$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpcuw6t_2m,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp53saqrze,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second,target=/GbFKKR/second_read_only_file,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmplrle3l4j/third,target=/my_path/third_writable_file \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth,target=/my_other_path/fourth_read_only_file,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth,target=/GbFKKR/sixth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpexcc8cx6/seventh,target=/my_path/seventh_writable_directory \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth,target=/my_other_path/eighth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmp07iolrgq/tenth_writable_directory_literal,target=/my_path/tenth_writable_directory_literal \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh,target=/GbFKKR/eleventh,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth,target=/GbFKKR/twelfth,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmphpy30rjt/my_file_literal,target=/my_path/my_file_literal,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp321qi8_g/20230605095036-465384.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n --env=LC_ALL=C \\\n docker.io/debian:stable-slim \\\n bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\necho "a" > first_writable_file\necho "b" > /my_path/third_writable_file\ntouch fifth_writable_directory/c\ntouch /my_path/seventh_writable_directory/d\nfind . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\n\' > /private/tmp/docker_tmpcuw6t_2m/log.txt\nINFO cwltool:job.py:905 [job iwdr_permutations.cwl_2] Max memory used: 0MiB\nERROR cwltool:job.py:395 Exception while running job\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 373, in _execute\n relink_initialworkdir(\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 103, in relink_initialworkdir\n shutil.rmtree(host_outdir_tgt)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 731, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 729, in rmtree\n os.rmdir(path)\nPermissionError: [Errno 13] Permission denied: \'/private/tmp/docker_tmpcuw6t_2m/sixth_read_only_directory\'\nWARNING cwltool:job.py:417 [job iwdr_permutations.cwl_2] completed permanentFail\nDEBUG cwltool:job.py:422 [job iwdr_permutations.cwl_2] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr_permutations.cwl_2] Removing input staging directory /private/tmp/docker_tmpy75vxspv\nDEBUG cwltool:job.py:454 [job iwdr_permutations.cwl_2] Removing temporary directory /private/tmp/docker_tmp53saqrze\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcuw6t_2m\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 2.665249376999782, 'start': 1685951434.82463, 'stop': 1685951437.489815, '$report_type': 'TestReport', 'item_index': 398, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_inplace', 'location': ('tests/test_iwdr.py', 188, 'test_iwdr_permutations_inplace'), 'keywords': {'test_iwdr_permutations_inplace': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl",\n "eighth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth"\n },\n "eleventh": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth"\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first"\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth"\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": []\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second"\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth"\n },\n "tenth": {\n "class": "Directory",\n "basename": "bar",\n "listing": []\n },\n "third": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr_permutations.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr_permutations.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr_permutations.cwl_2] {\n "eighth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth",\n "basename": "eighth"\n },\n "eleventh": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh",\n "size": 0,\n "basename": "eleventh",\n "nameroot": "eleventh",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "size": 0,\n "basename": "twelfth",\n "nameroot": "twelfth",\n "nameext": ""\n }\n ],\n "fifth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "basename": "fifth"\n },\n "first": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "size": 0,\n "basename": "first",\n "nameroot": "first",\n "nameext": ""\n },\n "fourth": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "size": 0,\n "basename": "fourth",\n "nameroot": "fourth",\n "nameext": ""\n },\n "ninth": {\n "class": "Directory",\n "basename": "foo",\n "listing": [],\n "location": "_:0b3439f5-e916-4bb0-875b-01251ced359b"\n },\n "second": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "size": 0,\n "basename": "second",\n "nameroot": "second",\n "nameext": ""\n },\n "seventh": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "basename": "seventh"\n },\n "sixth": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "basename": "sixth"\n },\n "tenth": {\n "class": "Directory",\n "basename": "bar",\n "listing": [],\n "location": "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b"\n },\n "third": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third",\n "size": 0,\n "basename": "third",\n "nameroot": "third",\n "nameext": ""\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr_permutations.cwl_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth",\n "/my_other_path/eighth_read_only_directory",\n "Directory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh",\n "/GbFKKR/eleventh",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "/GbFKKR/twelfth",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n false\n ],\n "_:0b3439f5-e916-4bb0-875b-01251ced359b": [\n "_:0b3439f5-e916-4bb0-875b-01251ced359b",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "/GbFKKR/second_read_only_file",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "/GbFKKR/sixth_read_only_directory",\n "Directory",\n false\n ],\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b": [\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third",\n "/my_path/third_writable_file",\n "WritableFile",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr_permutations.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "find . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\necho \\"a\\" > first_writable_file\\necho \\"b\\" > /my_path/third_writable_file\\ntouch fifth_writable_directory/c\\ntouch /my_path/seventh_writable_directory/d\\nfind . | grep -v \'\\\\.docker\' | sort\\nfind /my_path | sort\\nfind /my_other_path | sort\\n"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr_permutations.cwl_2] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/first",\n "/GbFKKR/first_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second",\n "/GbFKKR/second_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/third",\n "/my_path/third_writable_file",\n "WritableFile",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth",\n "/my_other_path/fourth_read_only_file",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fifth",\n "/GbFKKR/fifth_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth",\n "/GbFKKR/sixth_read_only_directory",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/seventh",\n "/my_path/seventh_writable_directory",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth",\n "/my_other_path/eighth_read_only_directory",\n "Directory",\n true\n ],\n "_:0b3439f5-e916-4bb0-875b-01251ced359b": [\n "_:0b3439f5-e916-4bb0-875b-01251ced359b",\n "/GbFKKR/nineth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b": [\n "_:c12bc1fd-883e-4b93-9e34-e2ba49a93e7b",\n "/my_path/tenth_writable_directory_literal",\n "WritableDirectory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh",\n "/GbFKKR/eleventh",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth",\n "/GbFKKR/twelfth",\n "File",\n true\n ],\n "_:b05fb645-e5b4-4261-ac08-84f2dbf2f4d6": [\n "baz",\n "/my_path/my_file_literal",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr_permutations.cwl_2] /private/tmp/docker_tmpcuw6t_2m$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpcuw6t_2m,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp53saqrze,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/second,target=/GbFKKR/second_read_only_file,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmplrle3l4j/third,target=/my_path/third_writable_file \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/fourth,target=/my_other_path/fourth_read_only_file,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/sixth,target=/GbFKKR/sixth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmpexcc8cx6/seventh,target=/my_path/seventh_writable_directory \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eighth,target=/my_other_path/eighth_read_only_directory,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmp07iolrgq/tenth_writable_directory_literal,target=/my_path/tenth_writable_directory_literal \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/eleventh,target=/GbFKKR/eleventh,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/misc2/twelfth,target=/GbFKKR/twelfth,readonly \\\n --mount=type=bind,source=/private/tmp/docker_tmphpy30rjt/my_file_literal,target=/my_path/my_file_literal,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp321qi8_g/20230605095036-465384.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n --env=LC_ALL=C \\\n docker.io/debian:stable-slim \\\n bash \\\n -c \\\n \'find . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\necho "a" > first_writable_file\necho "b" > /my_path/third_writable_file\ntouch fifth_writable_directory/c\ntouch /my_path/seventh_writable_directory/d\nfind . | grep -v \'"\'"\'\\.docker\'"\'"\' | sort\nfind /my_path | sort\nfind /my_other_path | sort\n\' > /private/tmp/docker_tmpcuw6t_2m/log.txt\nINFO cwltool:job.py:905 [job iwdr_permutations.cwl_2] Max memory used: 0MiB\nERROR cwltool:job.py:395 Exception while running job\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 373, in _execute\n relink_initialworkdir(\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 103, in relink_initialworkdir\n shutil.rmtree(host_outdir_tgt)\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 731, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File "/usr/local/Cellar/python@3.10/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/shutil.py", line 729, in rmtree\n os.rmdir(path)\nPermissionError: [Errno 13] Permission denied: \'/private/tmp/docker_tmpcuw6t_2m/sixth_read_only_directory\'\nWARNING cwltool:job.py:417 [job iwdr_permutations.cwl_2] completed permanentFail\nDEBUG cwltool:job.py:422 [job iwdr_permutations.cwl_2] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr_permutations.cwl_2] Removing input staging directory /private/tmp/docker_tmpy75vxspv\nDEBUG cwltool:job.py:454 [job iwdr_permutations.cwl_2] Removing temporary directory /private/tmp/docker_tmp53saqrze\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcuw6t_2m\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.0014437290001296788, 'start': 1685951437.5007098, 'stop': 1685951437.502156, '$report_type': 'TestReport', 'item_index': 398, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_iwdr.py::test_iwdr_permutations_inplace - location: ('tests/test_iwdr.py', 188, 'test_iwdr_permutations_inplace') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_iwdr.py::test_iwdr_permutations_singularity - location: ('tests/test_iwdr.py', 249, 'test_iwdr_permutations_singularity') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_singularity', 'location': ('tests/test_iwdr.py', 249, 'test_iwdr_permutations_singularity'), 'keywords': {'test_iwdr_permutations_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 250, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000361376000000746, 'start': 1685951437.5041401, 'stop': 1685951437.504503, '$report_type': 'TestReport', 'item_index': 399, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_singularity', 'location': ('tests/test_iwdr.py', 249, 'test_iwdr_permutations_singularity'), 'keywords': {'test_iwdr_permutations_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00029616200026794104, 'start': 1685951437.505357, 'stop': 1685951437.505656, '$report_type': 'TestReport', 'item_index': 399, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_iwdr.py::test_iwdr_permutations_singularity - location: ('tests/test_iwdr.py', 249, 'test_iwdr_permutations_singularity') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_iwdr.py::test_iwdr_permutations_singularity_inplace - location: ('tests/test_iwdr.py', 313, 'test_iwdr_permutations_singularity_inplace') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_singularity_inplace', 'location': ('tests/test_iwdr.py', 313, 'test_iwdr_permutations_singularity_inplace'), 'keywords': {'test_iwdr_permutations_singularity_inplace': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_iwdr.py', 314, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005646749996230938, 'start': 1685951437.507093, 'stop': 1685951437.507661, '$report_type': 'TestReport', 'item_index': 400, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_iwdr_permutations_singularity_inplace', 'location': ('tests/test_iwdr.py', 313, 'test_iwdr_permutations_singularity_inplace'), 'keywords': {'test_iwdr_permutations_singularity_inplace': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004171069995209109, 'start': 1685951437.508895, 'stop': 1685951437.509314, '$report_type': 'TestReport', 'item_index': 400, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_iwdr.py::test_iwdr_permutations_singularity_inplace - location: ('tests/test_iwdr.py', 313, 'test_iwdr_permutations_singularity_inplace') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_js_sandbox.py::test_node_version[v0.8.26\n-False] - location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.8.26\\n-False]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_js_sandbox.py::test_node_version[v0.8.26\\n-False]', 'location': ('tests/test_js_sandbox.py', 28, 'test_node_version[v0.8.26\\n-False]'), 'keywords': {'test_node_version[v0.8.26\\n-False]': 1, 'parametrize': 1, 'pytestmark': 1, 'v0.8.26\\n-False': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011338710000927676, 'start': 1685951437.510889, 'stop': 1685951437.512025, '$report_type': 'TestReport', 'item_index': 401, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: 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tests/test_js_sandbox.py::test_node_version[v7.7.3\n-True] - location: ('tests/test_js_sandbox.py', 28, 'test_node_version[v7.7.3\\n-True]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions - location: ('tests/test_js_sandbox.py', 36, 'test_value_from_two_concatenated_expressions') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions', 'location': ('tests/test_js_sandbox.py', 36, 'test_value_from_two_concatenated_expressions'), 'keywords': {'test_value_from_two_concatenated_expressions': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002535580006224336, 'start': 1685951437.535306, 'stop': 1685951437.5355608, '$report_type': 'TestReport', 'item_index': 406, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method_no_iteration', 'location': ('tests/test_loop.py', 174, 'test_loop_with_all_output_method_no_iteration'), 'keywords': {'test_loop_with_all_output_method_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/all-output-loop-no-iteration.cwl:25:7: object id 'tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _7] start\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step subworkflow_2\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _7] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/all-output-loop-no-iteration.cwl:25:7: object id \'tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step subworkflow_2\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_2] loop condition $(inputs.i1 < 1) evaluated to False at iteration 0\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_2] inputs was {\n "i1": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/o1": []\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _7] outputs {\n "o1": []\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa1ulhxe7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9535392379993937, 'start': 1685951436.7428648, 'stop': 1685951437.696382, '$report_type': 'TestReport', 'item_index': 433, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_with_all_output_method_no_iteration', 'location': ('tests/test_loop.py', 174, 'test_loop_with_all_output_method_no_iteration'), 'keywords': {'test_loop_with_all_output_method_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/all-output-loop-no-iteration.cwl:25:7: object id 'tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _7] start\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step subworkflow_2\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _7] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/all-output-loop-no-iteration.cwl:25:7: object id \'tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl\nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step subworkflow_2\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_2] loop condition $(inputs.i1 < 1) evaluated to False at iteration 0\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_2] inputs was {\n "i1": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/all-output-loop-no-iteration.cwl#subworkflow/o1": []\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _7] outputs {\n "o1": []\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa1ulhxe7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00035875300000043353, 'start': 1685951437.6971169, 'stop': 1685951437.6974778, '$report_type': 'TestReport', 'item_index': 433, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_loop_with_all_output_method_no_iteration - location: ('tests/test_loop.py', 174, 'test_loop_with_all_output_method_no_iteration') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_value_from', 'location': ('tests/test_loop.py', 187, 'test_loop_value_from'), 'keywords': {'test_loop_value_from': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002861479997591232, 'start': 1685951437.698797, 'stop': 1685951437.699084, '$report_type': 'TestReport', 'item_index': 434, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_loop_value_from - location: ('tests/test_loop.py', 187, 'test_loop_value_from') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_warn_large_inputs', 'location': ('tests/test_ext.py', 264, 'test_warn_large_inputs'), 'keywords': {'test_warn_large_inputs': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', '/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\'\nWARNING cwltool:process.py:795 tests/wf/listing_v1_0.cwl:5:3: Recursive directory listing has resulted in a large number of File\n objects (5) passed to the input parameter \'d\'. This may negatively\n affect workflow performance and memory use.\n \n If this is a problem, use the hint \'cwltool:LoadListingRequirement\'\n with "shallow_listing" or "no_listing" to change the directory\n listing behavior:\n \n $namespaces:\n cwltool: "http://commonwl.org/cwltool#"\n hints:\n cwltool:LoadListingRequirement:\n loadListing: shallow_listing\n \nDEBUG cwltool:command_line_tool.py:982 [job listing_v1_0.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\nDEBUG cwltool:command_line_tool.py:988 [job listing_v1_0.cwl] {\n "d": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4",\n "basename": "tmp4",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha",\n "basename": "alpha",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta",\n "basename": "delta",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot",\n "basename": "foxtrot",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo",\n "basename": "echo",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker",\n "basename": "baker",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie",\n "basename": "charlie",\n "size": 0\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job listing_v1_0.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/foxtrot",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/echo",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/baker",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/charlie",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job listing_v1_0.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.d.listing[0].listing[0])"\n }\n]\nDEBUG cwltool:job.py:215 [job listing_v1_0.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job listing_v1_0.cwl] /private/tmp/docker_tmp546a07j8$ echo \\\n /private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job listing_v1_0.cwl] completed success\nDEBUG cwltool:job.py:422 [job listing_v1_0.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job listing_v1_0.cwl] Removing input staging directory /private/tmp/docker_tmpcpbuwmdl\nDEBUG cwltool:job.py:454 [job listing_v1_0.cwl] Removing temporary directory /private/tmp/docker_tmp24i8q5y1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp546a07j8\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.734424934999879, 'start': 1685951436.99087, 'stop': 1685951437.72528, '$report_type': 'TestReport', 'item_index': 379, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_warn_large_inputs', 'location': ('tests/test_ext.py', 264, 'test_warn_large_inputs'), 'keywords': {'test_warn_large_inputs': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', '/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\'\nWARNING cwltool:process.py:795 tests/wf/listing_v1_0.cwl:5:3: Recursive directory listing has resulted in a large number of File\n objects (5) passed to the input parameter \'d\'. This may negatively\n affect workflow performance and memory use.\n \n If this is a problem, use the hint \'cwltool:LoadListingRequirement\'\n with "shallow_listing" or "no_listing" to change the directory\n listing behavior:\n \n $namespaces:\n cwltool: "http://commonwl.org/cwltool#"\n hints:\n cwltool:LoadListingRequirement:\n loadListing: shallow_listing\n \nDEBUG cwltool:command_line_tool.py:982 [job listing_v1_0.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/listing_v1_0.cwl\nDEBUG cwltool:command_line_tool.py:988 [job listing_v1_0.cwl] {\n "d": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4",\n "basename": "tmp4",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha",\n "basename": "alpha",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta",\n "basename": "delta",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot",\n "basename": "foxtrot",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo",\n "basename": "echo",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker",\n "basename": "baker",\n "size": 0\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie",\n "basename": "charlie",\n "size": 0\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job listing_v1_0.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha",\n "Directory",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/delta",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/foxtrot",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/foxtrot",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/echo",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/echo",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/baker",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/baker",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie": [\n "/Users/jasperk/gitlab/cwltool/tests/tmp4/alpha/charlie",\n "/private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/charlie",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job listing_v1_0.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.d.listing[0].listing[0])"\n }\n]\nDEBUG cwltool:job.py:215 [job listing_v1_0.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job listing_v1_0.cwl] /private/tmp/docker_tmp546a07j8$ echo \\\n /private/tmp/docker_tmpcpbuwmdl/stgf9cc7b23-08bb-4752-a322-418847304c24/tmp4/alpha/delta\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job listing_v1_0.cwl] completed success\nDEBUG cwltool:job.py:422 [job listing_v1_0.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job listing_v1_0.cwl] Removing input staging directory /private/tmp/docker_tmpcpbuwmdl\nDEBUG cwltool:job.py:454 [job listing_v1_0.cwl] Removing temporary directory /private/tmp/docker_tmp24i8q5y1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp546a07j8\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0004214670007058885, 'start': 1685951437.726537, 'stop': 1685951437.726959, '$report_type': 'TestReport', 'item_index': 379, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_warn_large_inputs - location: ('tests/test_ext.py', 264, 'test_warn_large_inputs') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_fetch.py::test_fetcher - location: ('tests/test_fetch.py', 52, 'test_fetcher') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_fetcher', 'location': ('tests/test_fetch.py', 52, 'test_fetcher'), 'keywords': {'test_fetcher': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002361979995839647, 'start': 1685951437.728332, 'stop': 1685951437.728569, '$report_type': 'TestReport', 'item_index': 380, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_no_ext', 'location': ('tests/test_loop.py', 20, 'test_validate_loop_fail_no_ext'), 'keywords': {'test_validate_loop_fail_no_ext': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/single-var-loop.cwl:15:1: checking field 'steps'\ntests/loop/single-var-loop.cwl:16:3: checking object 'tests/loop/single-var-loop.cwl#subworkflow'\ntests/loop/single-var-loop.cwl:28:5: checking field 'requirements'\ntests/loop/single-var-loop.cwl:29:7: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#Loop'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/single-var-loop.cwl:15:1: checking field 'steps'\ntests/loop/single-var-loop.cwl:16:3: checking object 'tests/loop/single-var-loop.cwl#subworkflow'\ntests/loop/single-var-loop.cwl:28:5: checking field 'requirements'\ntests/loop/single-var-loop.cwl:29:7: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#Loop'")], 'duration': 0.9462879800003066, 'start': 1685951436.9938939, 'stop': 1685951437.94016, '$report_type': 'TestReport', 'item_index': 419, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_no_ext', 'location': ('tests/test_loop.py', 20, 'test_validate_loop_fail_no_ext'), 'keywords': {'test_validate_loop_fail_no_ext': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/single-var-loop.cwl:15:1: checking field 'steps'\ntests/loop/single-var-loop.cwl:16:3: checking object 'tests/loop/single-var-loop.cwl#subworkflow'\ntests/loop/single-var-loop.cwl:28:5: checking field 'requirements'\ntests/loop/single-var-loop.cwl:29:7: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#Loop'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/single-var-loop.cwl:15:1: checking field 'steps'\ntests/loop/single-var-loop.cwl:16:3: checking object 'tests/loop/single-var-loop.cwl#subworkflow'\ntests/loop/single-var-loop.cwl:28:5: checking field 'requirements'\ntests/loop/single-var-loop.cwl:29:7: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#Loop'")], 'duration': 0.0003070539996770094, 'start': 1685951437.94085, 'stop': 1685951437.941161, '$report_type': 'TestReport', 'item_index': 419, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_validate_loop_fail_no_ext - location: ('tests/test_loop.py', 20, 'test_validate_loop_fail_no_ext') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_validate_loop_fail_scatter - location: ('tests/test_loop.py', 29, 'test_validate_loop_fail_scatter') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_scatter', 'location': ('tests/test_loop.py', 29, 'test_validate_loop_fail_scatter'), 'keywords': {'test_validate_loop_fail_scatter': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004007010002169409, 'start': 1685951437.9424949, 'stop': 1685951437.9428968, '$report_type': 'TestReport', 'item_index': 420, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions', 'location': ('tests/test_js_sandbox.py', 36, 'test_value_from_two_concatenated_expressions'), 'keywords': {'test_value_from_two_concatenated_expressions': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\'\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "valueFrom": "$(\\"a \\")$(\\"string\\")",\n "position": [\n 0,\n "file1"\n ],\n "datum": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "dirname": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066"\n }\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mINFO\x1b[0m [job vf-concat.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c$ echo \\\n \'a string\' > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c/output.txt\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mINFO\x1b[0m [job vf-concat.cwl] completed success\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] outputs {\n "out": "a string\\n"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/epq_ftst\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job vf-concat.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\nDEBUG cwltool:command_line_tool.py:988 [job vf-concat.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job vf-concat.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job vf-concat.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "valueFrom": "$(\\"a \\")$(\\"string\\")",\n "position": [\n 0,\n "file1"\n ],\n "datum": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "dirname": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job vf-concat.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job vf-concat.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c$ echo \\\n \'a string\' > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job vf-concat.cwl] completed success\nDEBUG cwltool:job.py:422 [job vf-concat.cwl] outputs {\n "out": "a string\\n"\n}\nDEBUG cwltool:job.py:446 [job vf-concat.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es\nDEBUG cwltool:job.py:454 [job vf-concat.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/epq_ftst\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c')], 'duration': 0.5434311580002031, 'start': 1685951437.53597, 'stop': 1685951438.07939, '$report_type': 'TestReport', 'item_index': 406, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions', 'location': ('tests/test_js_sandbox.py', 36, 'test_value_from_two_concatenated_expressions'), 'keywords': {'test_value_from_two_concatenated_expressions': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\'\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "valueFrom": "$(\\"a \\")$(\\"string\\")",\n "position": [\n 0,\n "file1"\n ],\n "datum": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "dirname": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066"\n }\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mINFO\x1b[0m [job vf-concat.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c$ echo \\\n \'a string\' > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c/output.txt\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mINFO\x1b[0m [job vf-concat.cwl] completed success\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] outputs {\n "out": "a string\\n"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job vf-concat.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/epq_ftst\x1b[0m\n\x1b[32m[2023-06-05 09:50:38]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job vf-concat.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/vf-concat.cwl\nDEBUG cwltool:command_line_tool.py:988 [job vf-concat.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job vf-concat.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job vf-concat.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "valueFrom": "$(\\"a \\")$(\\"string\\")",\n "position": [\n 0,\n "file1"\n ],\n "datum": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066/whale.txt",\n "dirname": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es/stg989d68f1-35ac-4198-b06d-290db81c3066"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job vf-concat.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job vf-concat.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c$ echo \\\n \'a string\' > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job vf-concat.cwl] completed success\nDEBUG cwltool:job.py:422 [job vf-concat.cwl] outputs {\n "out": "a string\\n"\n}\nDEBUG cwltool:job.py:446 [job vf-concat.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/nrke01es\nDEBUG cwltool:job.py:454 [job vf-concat.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/epq_ftst\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/xmn2xp3c')], 'duration': 0.0004654399999708403, 'start': 1685951438.0806642, 'stop': 1685951438.081131, '$report_type': 'TestReport', 'item_index': 406, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions - location: ('tests/test_js_sandbox.py', 36, 'test_value_from_two_concatenated_expressions') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_podman - location: ('tests/test_js_sandbox.py', 72, 'test_value_from_two_concatenated_expressions_podman') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_podman', 'location': ('tests/test_js_sandbox.py', 72, 'test_value_from_two_concatenated_expressions_podman'), 'keywords': {'test_value_from_two_concatenated_expressions_podman': 1, 'skipif': 1, 'pytestmark': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_js_sandbox.py', 73, 'Skipped: Requires the podman executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00030104899997240864, 'start': 1685951438.08305, 'stop': 1685951438.083353, '$report_type': 'TestReport', 'item_index': 407, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_podman', 'location': ('tests/test_js_sandbox.py', 72, 'test_value_from_two_concatenated_expressions_podman'), 'keywords': {'test_value_from_two_concatenated_expressions_podman': 1, 'skipif': 1, 'pytestmark': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00024386600034631556, 'start': 1685951438.084286, 'stop': 1685951438.0845308, '$report_type': 'TestReport', 'item_index': 407, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_podman - location: ('tests/test_js_sandbox.py', 72, 'test_value_from_two_concatenated_expressions_podman') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_singularity - location: ('tests/test_js_sandbox.py', 92, 'test_value_from_two_concatenated_expressions_singularity') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_singularity', 'location': ('tests/test_js_sandbox.py', 92, 'test_value_from_two_concatenated_expressions_singularity'), 'keywords': {'test_value_from_two_concatenated_expressions_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_js_sandbox.py', 93, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00024004999977478292, 'start': 1685951438.08574, 'stop': 1685951438.085981, '$report_type': 'TestReport', 'item_index': 408, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_singularity', 'location': ('tests/test_js_sandbox.py', 92, 'test_value_from_two_concatenated_expressions_singularity'), 'keywords': {'test_value_from_two_concatenated_expressions_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_js_sandbox.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00024955099979706574, 'start': 1685951438.0868962, 'stop': 1685951438.087147, '$report_type': 'TestReport', 'item_index': 408, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_js_sandbox.py::test_value_from_two_concatenated_expressions_singularity - location: ('tests/test_js_sandbox.py', 92, 'test_value_from_two_concatenated_expressions_singularity') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_multi_source_loop_input_fail_no_requirement - location: ('tests/test_loop.py', 262, 'test_multi_source_loop_input_fail_no_requirement') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input_fail_no_requirement', 'location': ('tests/test_loop.py', 262, 'test_multi_source_loop_input_fail_no_requirement'), 'keywords': {'test_multi_source_loop_input_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00029997300043760333, 'start': 1685951438.0884101, 'stop': 1685951438.088712, '$report_type': 'TestReport', 'item_index': 440, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_fetcher', 'location': ('tests/test_fetch.py', 52, 'test_fetcher'), 'keywords': {'test_fetcher': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "baseCommand": "echo",\n "class": "CommandLineTool",\n "cwlVersion": "v1.0",\n "id": "baz:bar/foo.cwl#bar/foo.cwl",\n "inputs": [],\n "outputs": []\n}'), ('Captured stderr call', "\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?")], 'duration': 0.715932681000595, 'start': 1685951437.7290199, 'stop': 1685951438.444936, '$report_type': 'TestReport', 'item_index': 380, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_fetcher', 'location': ('tests/test_fetch.py', 52, 'test_fetcher'), 'keywords': {'test_fetcher': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "baseCommand": "echo",\n "class": "CommandLineTool",\n "cwlVersion": "v1.0",\n "id": "baz:bar/foo.cwl#bar/foo.cwl",\n "inputs": [],\n "outputs": []\n}'), ('Captured stderr call', "\x1b[32m[2023-06-05 09:50:37]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nURI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved 'foo.cwl' to 'baz:bar/foo.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:240 URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section?")], 'duration': 0.0003046749998247833, 'start': 1685951438.445558, 'stop': 1685951438.445864, '$report_type': 'TestReport', 'item_index': 380, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_fetch.py::test_fetcher - location: ('tests/test_fetch.py', 52, 'test_fetcher') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_fetch.py::test_resolve_local[tests/echo.cwl-/tests/echo.cwl] - location: ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006597010005862103, 'start': 1685951438.4470139, 'stop': 1685951438.447675, '$report_type': 'TestReport', 'item_index': 381, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006710289999318775, 'start': 1685951438.448179, 'stop': 1685951438.448852, '$report_type': 'TestReport', 'item_index': 381, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00039458500032196753, 'start': 1685951438.449436, 'stop': 1685951438.449832, '$report_type': 'TestReport', 'item_index': 381, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_fetch.py::test_resolve_local[tests/echo.cwl-/tests/echo.cwl] - location: ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl-/tests/echo.cwl]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_fetch.py::test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main] - location: ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006498700004158309, 'start': 1685951438.4510012, 'stop': 1685951438.451652, '$report_type': 'TestReport', 'item_index': 382, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005966490007267566, 'start': 1685951438.452197, 'stop': 1685951438.4527948, '$report_type': 'TestReport', 'item_index': 382, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00036924100004398497, 'start': 1685951438.453301, 'stop': 1685951438.453671, '$report_type': 'TestReport', 'item_index': 382, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_fetch.py::test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main] - location: ('tests/test_fetch.py', 81, 'test_resolve_local[tests/echo.cwl#main-/tests/echo.cwl#main]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl] - location: ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005771220003225608, 'start': 1685951438.4548259, 'stop': 1685951438.455405, '$report_type': 'TestReport', 'item_index': 383, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006573210002898122, 'start': 1685951438.4559438, 'stop': 1685951438.456602, '$report_type': 'TestReport', 'item_index': 383, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005036920001657563, 'start': 1685951438.457206, 'stop': 1685951438.4577112, '$report_type': 'TestReport', 'item_index': 383, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl] - location: ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl-/tests/echo.cwl]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main] - location: ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007643929993719212, 'start': 1685951438.459253, 'stop': 1685951438.4600189, '$report_type': 'TestReport', 'item_index': 384, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006920289997651707, 'start': 1685951438.460586, 'stop': 1685951438.46128, '$report_type': 'TestReport', 'item_index': 384, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]', 'location': ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]'), 'keywords': {'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]': 1, 'parametrize': 1, 'pytestmark': 1, '/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main': 1, 'test_fetch.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00026139400051761186, 'start': 1685951438.461681, 'stop': 1685951438.461944, '$report_type': 'TestReport', 'item_index': 384, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_fetch.py::test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main] - location: ('tests/test_fetch.py', 81, 'test_resolve_local[/Users/jasperk/gitlab/cwltool/tests/echo.cwl#main-/tests/echo.cwl#main]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_http_input.py::test_http_path_mapping - location: ('tests/test_http_input.py', 13, 'test_http_path_mapping') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_http_input.py::test_http_path_mapping', 'location': ('tests/test_http_input.py', 13, 'test_http_path_mapping'), 'keywords': {'test_http_path_mapping': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014472699995167204, 'start': 1685951438.462792, 'stop': 1685951438.46424, '$report_type': 'TestReport', 'item_index': 385, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_http_input.py::test_http_path_mapping', 'location': ('tests/test_http_input.py', 13, 'test_http_path_mapping'), 'keywords': {'test_http_path_mapping': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.003667699999823526, 'start': 1685951438.464559, 'stop': 1685951438.468228, '$report_type': 'TestReport', 'item_index': 385, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_http_input.py::test_http_path_mapping', 'location': ('tests/test_http_input.py', 13, 'test_http_path_mapping'), 'keywords': {'test_http_path_mapping': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00032206000014411984, 'start': 1685951438.468769, 'stop': 1685951438.469093, '$report_type': 'TestReport', 'item_index': 385, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_http_input.py::test_http_path_mapping - location: ('tests/test_http_input.py', 13, 'test_http_path_mapping') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_http_input.py::test_modification_date - location: ('tests/test_http_input.py', 36, 'test_modification_date') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_http_input.py::test_modification_date', 'location': ('tests/test_http_input.py', 36, 'test_modification_date'), 'keywords': {'test_modification_date': 1, 'skipif': 1, 'pytestmark': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008432869999523973, 'start': 1685951438.47001, 'stop': 1685951438.4708538, '$report_type': 'TestReport', 'item_index': 386, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--debug]'), 'keywords': {'test_cache_relative_paths[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_5] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_5] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_5] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_5] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmp47n97al1/stgb620e7cc-3aa3-4431-ae41-b9e220a3c7c3/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmp47n97al1/stgb620e7cc-3aa3-4431-ae41-b9e220a3c7c3/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job secondary-files.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_5] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_5] Removing input staging directory /private/tmp/docker_tmp47n97al1\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_5] Removing temporary directory /private/tmp/docker_tmpkmqmkc1i\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cacheqsaiiuf2\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_6] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_6] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cachekzcrurqy\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.7288621939997029, 'start': 1685951436.8263628, 'stop': 1685951438.5551841, '$report_type': 'TestReport', 'item_index': 302, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--debug]'), 'keywords': {'test_cache_relative_paths[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_5] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_5] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_5] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_5] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmp47n97al1/stgb620e7cc-3aa3-4431-ae41-b9e220a3c7c3/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmp47n97al1/stgb620e7cc-3aa3-4431-ae41-b9e220a3c7c3/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job secondary-files.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_5] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_5] Removing input staging directory /private/tmp/docker_tmp47n97al1\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_5] Removing temporary directory /private/tmp/docker_tmpkmqmkc1i\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cacheqsaiiuf2\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_6] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_6] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___de0/cwltool_cachekzcrurqy\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005429989996628137, 'start': 1685951438.555991, 'stop': 1685951438.556535, '$report_type': 'TestReport', 'item_index': 302, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cache_relative_paths[--debug] - location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--debug]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cache_relative_paths[--parallel --debug] - location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel --debug]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel --debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel --debug]'), 'keywords': {'test_cache_relative_paths[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016512539996256237, 'start': 1685951438.558201, 'stop': 1685951438.559854, '$report_type': 'TestReport', 'item_index': 303, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_double_overwrite', 'location': ('tests/test_ext.py', 76, 'test_double_overwrite'), 'keywords': {'test_double_overwrite': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m [workflow ] start\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/python:3-slim']\n3-slim: Pulling from library/python\nDigest: sha256:eaee5f73efa9ae962d2077756292bc4878c04fcbc13dc168bb00cc365f35647e\nStatus: Image is up to date for python:3-slim\ndocker.io/library/python:3-slim\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmp_30_j4_2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_30_j4_2,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpb8gbxko8,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkj57te9v/20230605095036-573055.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step1] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step step2\n\x1b[1;30mINFO\x1b[0m [step step2] start\n\x1b[1;30mINFO\x1b[0m [job step2] /private/tmp/docker_tmp9iy54f2l$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp9iy54f2l,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqpnyw3w,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphp0i1stc/20230605095037-615502.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step2] completed success\n\x1b[1;30mINFO\x1b[0m [step step2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow ] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl",\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value"\n }\n}\nDEBUG cwltool:workflow_job.py:498 [workflow ] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\nINFO cwltool:workflow_job.py:765 [workflow ] start\nDEBUG cwltool:workflow_job.py:777 [workflow ] inputs {\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow ] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/python:3-slim\']\nDEBUG cwltool:job.py:215 [job step1] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp_30_j4_2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_30_j4_2,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpb8gbxko8,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkj57te9v/20230605095036-573055.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpm2j47r1m\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpb8gbxko8\nINFO cwltool:workflow_job.py:613 [workflow ] starting step step2\nDEBUG cwltool:workflow_job.py:727 [step step2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2] start\nDEBUG cwltool:command_line_tool.py:982 [job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step2\nDEBUG cwltool:command_line_tool.py:988 [job step2] {\n "r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step2] path mappings is {\n "file:///private/tmp/docker_tmp_30_j4_2/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job step2] initial work dir {\n "file:///private/tmp/docker_tmp_30_j4_2/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step2] /private/tmp/docker_tmp9iy54f2l$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp9iy54f2l,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqpnyw3w,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphp0i1stc/20230605095037-615502.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step2] completed success\nDEBUG cwltool:job.py:422 [job step2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2] completed success\nINFO cwltool:workflow_job.py:539 [workflow ] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow ] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step2] Removing input staging directory /private/tmp/docker_tmpe8awqq_l\nDEBUG cwltool:job.py:454 [job step2] Removing temporary directory /private/tmp/docker_tmpdqpnyw3w\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_30_j4_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9iy54f2l\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpflv_h189\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 5.5616510429999835, 'start': 1685951433.0829089, 'stop': 1685951438.644423, '$report_type': 'TestReport', 'item_index': 369, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_double_overwrite', 'location': ('tests/test_ext.py', 76, 'test_double_overwrite'), 'keywords': {'test_double_overwrite': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m [workflow ] start\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/python:3-slim']\n3-slim: Pulling from library/python\nDigest: sha256:eaee5f73efa9ae962d2077756292bc4878c04fcbc13dc168bb00cc365f35647e\nStatus: Image is up to date for python:3-slim\ndocker.io/library/python:3-slim\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmp_30_j4_2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_30_j4_2,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpb8gbxko8,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkj57te9v/20230605095036-573055.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step1] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step step2\n\x1b[1;30mINFO\x1b[0m [step step2] start\n\x1b[1;30mINFO\x1b[0m [job step2] /private/tmp/docker_tmp9iy54f2l$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp9iy54f2l,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqpnyw3w,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphp0i1stc/20230605095037-615502.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step2] completed success\n\x1b[1;30mINFO\x1b[0m [step step2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow ] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl",\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value"\n }\n}\nDEBUG cwltool:workflow_job.py:498 [workflow ] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl\nINFO cwltool:workflow_job.py:765 [workflow ] start\nDEBUG cwltool:workflow_job.py:777 [workflow ] inputs {\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow ] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/python:3-slim\']\nDEBUG cwltool:job.py:215 [job step1] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp_30_j4_2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_30_j4_2,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpb8gbxko8,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpkj57te9v/20230605095036-573055.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg46c74d9e-5417-40a9-85dc-35bd6682a795/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpm2j47r1m\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpb8gbxko8\nINFO cwltool:workflow_job.py:613 [workflow ] starting step step2\nDEBUG cwltool:workflow_job.py:727 [step step2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2] start\nDEBUG cwltool:command_line_tool.py:982 [job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step2\nDEBUG cwltool:command_line_tool.py:988 [job step2] {\n "r": {\n "location": "file:///private/tmp/docker_tmp_30_j4_2/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step2] path mappings is {\n "file:///private/tmp/docker_tmp_30_j4_2/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job step2] initial work dir {\n "file:///private/tmp/docker_tmp_30_j4_2/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step2] /private/tmp/docker_tmp9iy54f2l$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp9iy54f2l,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqpnyw3w,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphp0i1stc/20230605095037-615502.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg07bb8480-37d6-4428-bde8-f64926beb206/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step2] completed success\nDEBUG cwltool:job.py:422 [job step2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut2.cwl#step2/out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2] completed success\nINFO cwltool:workflow_job.py:539 [workflow ] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow ] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9iy54f2l/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$77de68daecd823babbb58edb1c8e14d7106e83bb",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step2] Removing input staging directory /private/tmp/docker_tmpe8awqq_l\nDEBUG cwltool:job.py:454 [job step2] Removing temporary directory /private/tmp/docker_tmpdqpnyw3w\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/value to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_double_overwrite0/outdir/value\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_30_j4_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9iy54f2l\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpflv_h189\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005781970003226888, 'start': 1685951438.645545, 'stop': 1685951438.646125, '$report_type': 'TestReport', 'item_index': 369, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_double_overwrite - location: ('tests/test_ext.py', 76, 'test_double_overwrite') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_ext.py::test_disable_file_overwrite_without_ext - location: ('tests/test_ext.py', 106, 'test_disable_file_overwrite_without_ext') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_file_overwrite_without_ext', 'location': ('tests/test_ext.py', 106, 'test_disable_file_overwrite_without_ext'), 'keywords': {'test_disable_file_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018297330007044366, 'start': 1685951438.64766, 'stop': 1685951438.649492, '$report_type': 'TestReport', 'item_index': 370, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_value_from', 'location': ('tests/test_loop.py', 187, 'test_loop_value_from'), 'keywords': {'test_loop_value_from': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/value-from-loop.cwl:28:7: object id 'tests/loop/value-from-loop.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _8] start\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step subworkflow_3\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _8] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/value-from-loop.cwl:28:7: object id \'tests/loop/value-from-loop.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _8] start\nDEBUG cwltool:workflow_job.py:777 [workflow _8] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step subworkflow_3\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_3] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_3] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _8] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaelm08fz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.057735744000638, 'start': 1685951437.699521, 'stop': 1685951438.7572322, '$report_type': 'TestReport', 'item_index': 434, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_value_from', 'location': ('tests/test_loop.py', 187, 'test_loop_value_from'), 'keywords': {'test_loop_value_from': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/value-from-loop.cwl:28:7: object id 'tests/loop/value-from-loop.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _8] start\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step subworkflow_3\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _8] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/value-from-loop.cwl:28:7: object id \'tests/loop/value-from-loop.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _8] start\nDEBUG cwltool:workflow_job.py:777 [workflow _8] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step subworkflow_3\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_3] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_3] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_3] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/value-from-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _8] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaelm08fz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00037351199989643646, 'start': 1685951438.758164, 'stop': 1685951438.758539, '$report_type': 'TestReport', 'item_index': 434, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_loop_value_from - location: ('tests/test_loop.py', 187, 'test_loop_value_from') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_loop_value_from_fail_no_requirement - location: ('tests/test_loop.py', 200, 'test_loop_value_from_fail_no_requirement') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_value_from_fail_no_requirement', 'location': ('tests/test_loop.py', 200, 'test_loop_value_from_fail_no_requirement'), 'keywords': {'test_loop_value_from_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003256449999753386, 'start': 1685951438.760072, 'stop': 1685951438.760399, '$report_type': 'TestReport', 'item_index': 435, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_scatter', 'location': ('tests/test_loop.py', 29, 'test_validate_loop_fail_scatter'), 'keywords': {'test_validate_loop_fail_scatter': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-scatter.cwl:32:11: object id 'tests/loop/invalid-loop-scatter.cwl#subworkflow/i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-scatter.cwl:18:3: The `cwltool:Loop` clause is not compatible with the\n `scatter` directive.\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-scatter.cwl:32:11: object id 'tests/loop/invalid-loop-scatter.cwl#subworkflow/i1' previously defined\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-scatter.cwl:18:3: The `cwltool:Loop` clause is not compatible with the\n `scatter` directive.")], 'duration': 0.9162313860006179, 'start': 1685951437.943309, 'stop': 1685951438.859519, '$report_type': 'TestReport', 'item_index': 420, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_scatter', 'location': ('tests/test_loop.py', 29, 'test_validate_loop_fail_scatter'), 'keywords': {'test_validate_loop_fail_scatter': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-scatter.cwl:32:11: object id 'tests/loop/invalid-loop-scatter.cwl#subworkflow/i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-scatter.cwl:18:3: The `cwltool:Loop` clause is not compatible with the\n `scatter` directive.\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-scatter.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-scatter.cwl:32:11: object id 'tests/loop/invalid-loop-scatter.cwl#subworkflow/i1' previously defined\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-scatter.cwl:18:3: The `cwltool:Loop` clause is not compatible with the\n `scatter` directive.")], 'duration': 0.0002120910003213794, 'start': 1685951438.860019, 'stop': 1685951438.8602319, '$report_type': 'TestReport', 'item_index': 420, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_when', 'location': ('tests/test_loop.py', 39, 'test_validate_loop_fail_when'), 'keywords': {'test_validate_loop_fail_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0001864279993242235, 'start': 1685951438.861054, 'stop': 1685951438.861241, '$report_type': 'TestReport', 'item_index': 421, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_validate_loop_fail_when - location: ('tests/test_loop.py', 39, 'test_validate_loop_fail_when') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_http_input.py::test_modification_date', 'location': ('tests/test_http_input.py', 36, 'test_modification_date'), 'keywords': {'test_modification_date': 1, 'skipif': 1, 'pytestmark': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO werkzeug:_internal.py:186 127.0.0.1 - - [05/Jun/2023 09:50:38] "GET /testfile.txt HTTP/1.1" 200 -')], 'duration': 0.5317395809997834, 'start': 1685951438.47117, 'stop': 1685951439.002898, '$report_type': 'TestReport', 'item_index': 386, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_http_input.py::test_modification_date', 'location': ('tests/test_http_input.py', 36, 'test_modification_date'), 'keywords': {'test_modification_date': 1, 'skipif': 1, 'pytestmark': 1, 'test_http_input.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO werkzeug:_internal.py:186 127.0.0.1 - - [05/Jun/2023 09:50:38] "GET /testfile.txt HTTP/1.1" 200 -')], 'duration': 0.00039448400002584094, 'start': 1685951439.003603, 'stop': 1685951439.003999, '$report_type': 'TestReport', 'item_index': 386, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_http_input.py::test_modification_date - location: ('tests/test_http_input.py', 36, 'test_modification_date') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_input_deps.py::test_input_deps - location: ('tests/test_input_deps.py', 13, 'test_input_deps') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_input_deps.py::test_input_deps', 'location': ('tests/test_input_deps.py', 13, 'test_input_deps'), 'keywords': {'test_input_deps': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002890409996325616, 'start': 1685951439.005383, 'stop': 1685951439.005673, '$report_type': 'TestReport', 'item_index': 387, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] -\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa0/cwltool_cacheyc1ic0v7\nINFO cwltool:main.py:13 pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input_fail_no_requirement', 'location': ('tests/test_loop.py', 262, 'test_multi_source_loop_input_fail_no_requirement'), 'keywords': {'test_multi_source_loop_input_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:59:7: object id \'tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:11: Source \'osmall\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:19: Source \'obig\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow ] start\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step loop\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step small_values\n\x1b[1;30mINFO\x1b[0m [step small_values] start\n\x1b[1;30mINFO\x1b[0m [step small_values] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step big_values\n\x1b[1;30mINFO\x1b[0m [step big_values] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 1 completed success\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step big_values] Cannot make job: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[step loop] completed permanentFail\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[workflow ] Cannot collect workflow output: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow ] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-multi-source-loop-no-requirement.cwl:59:7: object id \'tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:11: Source \'osmall\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:19: Source \'obig\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow ] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\nINFO cwltool:workflow_job.py:765 [workflow ] start\nDEBUG cwltool:workflow_job.py:777 [workflow ] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow ] starting step loop\nDEBUG cwltool:workflow_job.py:727 [step loop] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop] initialized from _:190467e8-291e-47f2-bb03-2b35d4dd8bb1\nINFO cwltool:workflow_job.py:765 [workflow loop] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step small_values\nDEBUG cwltool:workflow_job.py:727 [step small_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step small_values] start\nDEBUG cwltool:workflow_job.py:564 [step small_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step small_values] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step big_values\nDEBUG cwltool:workflow_job.py:727 [step big_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop] outputs {\n "obig": null,\n "osmall": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/osmall": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 1 completed success\nERROR cwltool:workflow_job.py:833 [step big_values] Cannot make job: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 745, in try_make_job\n callback({k["id"]: None for k in outputparms}, "skipped")\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 582, in receive_output\n self.do_output_callback(final_output_callback)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 545, in do_output_callback\n final_output_callback(wo, self.processStatus)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 429, in receive_output\n output_callback(output, processStatus)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 1020, in loop_callback\n object_from_state(\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 391, in object_from_state\n raise WorkflowException(\ncwltool.errors.WorkflowException: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nDEBUG cwltool:workflow_job.py:564 [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/osmall": [\n 2\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/obig": [\n null\n ]\n}\nWARNING cwltool:workflow_job.py:570 [step loop] completed permanentFail\nERROR cwltool:workflow_job.py:520 [workflow ] Cannot collect workflow output: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nINFO cwltool:workflow_job.py:539 [workflow ] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow ] outputs null\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7mewqrkl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp45f8r8g2\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 1.0215164639994327, 'start': 1685951438.089225, 'stop': 1685951439.110718, '$report_type': 'TestReport', 'item_index': 440, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input_fail_no_requirement', 'location': ('tests/test_loop.py', 262, 'test_multi_source_loop_input_fail_no_requirement'), 'keywords': {'test_multi_source_loop_input_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:59:7: object id \'tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:11: Source \'osmall\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:19: Source \'obig\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow ] start\n\x1b[1;30mINFO\x1b[0m [workflow ] starting step loop\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step small_values\n\x1b[1;30mINFO\x1b[0m [step small_values] start\n\x1b[1;30mINFO\x1b[0m [step small_values] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step big_values\n\x1b[1;30mINFO\x1b[0m [step big_values] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 1 completed success\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step big_values] Cannot make job: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[step loop] completed permanentFail\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[workflow ] Cannot collect workflow output: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow ] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-multi-source-loop-no-requirement.cwl:59:7: object id \'tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:11: Source \'osmall\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:60:19: Source \'obig\' of type {"type":\n "array", "items": ["null", "int"]}\n may be incompatible\ntests/loop/invalid-multi-source-loop-no-requirement.cwl:14:5: with sink \'o1\' of type {"type":\n "array", "items": "int"}\n source has linkMerge method\n merge_flattened\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow ] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl\nINFO cwltool:workflow_job.py:765 [workflow ] start\nDEBUG cwltool:workflow_job.py:777 [workflow ] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow ] starting step loop\nDEBUG cwltool:workflow_job.py:727 [step loop] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop] initialized from _:190467e8-291e-47f2-bb03-2b35d4dd8bb1\nINFO cwltool:workflow_job.py:765 [workflow loop] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step small_values\nDEBUG cwltool:workflow_job.py:727 [step small_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step small_values] start\nDEBUG cwltool:workflow_job.py:564 [step small_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/small_values/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step small_values] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step big_values\nDEBUG cwltool:workflow_job.py:727 [step big_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop] outputs {\n "obig": null,\n "osmall": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/osmall": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 1 completed success\nERROR cwltool:workflow_job.py:833 [step big_values] Cannot make job: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 745, in try_make_job\n callback({k["id"]: None for k in outputparms}, "skipped")\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 582, in receive_output\n self.do_output_callback(final_output_callback)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 545, in do_output_callback\n final_output_callback(wo, self.processStatus)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 429, in receive_output\n output_callback(output, processStatus)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 1020, in loop_callback\n object_from_state(\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 391, in object_from_state\n raise WorkflowException(\ncwltool.errors.WorkflowException: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nDEBUG cwltool:workflow_job.py:564 [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/osmall": [\n 2\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-multi-source-loop-no-requirement.cwl#loop/obig": [\n null\n ]\n}\nWARNING cwltool:workflow_job.py:570 [step loop] completed permanentFail\nERROR cwltool:workflow_job.py:520 [workflow ] Cannot collect workflow output: Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.\nINFO cwltool:workflow_job.py:539 [workflow ] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow ] outputs null\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7mewqrkl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp45f8r8g2\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.0006661150000581983, 'start': 1685951439.112205, 'stop': 1685951439.112873, '$report_type': 'TestReport', 'item_index': 440, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_multi_source_loop_input_fail_no_requirement - location: ('tests/test_loop.py', 262, 'test_multi_source_loop_input_fail_no_requirement') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_default_value_loop - location: ('tests/test_loop.py', 272, 'test_default_value_loop') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_default_value_loop', 'location': ('tests/test_loop.py', 272, 'test_default_value_loop'), 'keywords': {'test_default_value_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002949979998447816, 'start': 1685951439.114215, 'stop': 1685951439.114511, '$report_type': 'TestReport', 'item_index': 441, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_value_from_fail_no_requirement', 'location': ('tests/test_loop.py', 200, 'test_loop_value_from_fail_no_requirement'), 'keywords': {'test_loop_value_from_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-value-from-loop-no-requirement.cwl:27:7: object id 'tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _9] start\n\x1b[1;30mINFO\x1b[0m [workflow _9] starting step subworkflow_4\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 1 completed success\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFailed to evaluate expression:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step subworkflow_4] Output of iteration 2 is missing expected field file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[step subworkflow_4] Iteration 2 completed permanentFail\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-value-from-loop-no-requirement.cwl:27:7: object id \'tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step subworkflow_4\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 1 completed success\nWARNING cwltool:command_line_tool.py:204 Failed to evaluate expression:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\nERROR cwltool:workflow_job.py:979 [step subworkflow_4] Output of iteration 2 is missing expected field file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_4] produced output {}\nWARNING cwltool:workflow_job.py:998 [step subworkflow_4] Iteration 2 completed permanentFail\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements')], 'duration': 0.9961248460003844, 'start': 1685951438.760916, 'stop': 1685951439.7570171, '$report_type': 'TestReport', 'item_index': 435, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_value_from_fail_no_requirement', 'location': ('tests/test_loop.py', 200, 'test_loop_value_from_fail_no_requirement'), 'keywords': {'test_loop_value_from_fail_no_requirement': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-value-from-loop-no-requirement.cwl:27:7: object id 'tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _9] start\n\x1b[1;30mINFO\x1b[0m [workflow _9] starting step subworkflow_4\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 1 completed success\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFailed to evaluate expression:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step subworkflow_4] Output of iteration 2 is missing expected field file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[step subworkflow_4] Iteration 2 completed permanentFail\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-value-from-loop-no-requirement.cwl:27:7: object id \'tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl\nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step subworkflow_4\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 1 completed success\nWARNING cwltool:command_line_tool.py:204 Failed to evaluate expression:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements\nERROR cwltool:workflow_job.py:979 [step subworkflow_4] Output of iteration 2 is missing expected field file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-value-from-loop-no-requirement.cwl#subworkflow/o1\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_4] produced output {}\nWARNING cwltool:workflow_job.py:998 [step subworkflow_4] Iteration 2 completed permanentFail\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nWorkflow step contains valueFrom but StepInputExpressionRequirement not in requirements')], 'duration': 0.00036002799970447086, 'start': 1685951439.757768, 'stop': 1685951439.7581298, '$report_type': 'TestReport', 'item_index': 435, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_loop_value_from_fail_no_requirement - location: ('tests/test_loop.py', 200, 'test_loop_value_from_fail_no_requirement') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_loop_inside_scatter - location: ('tests/test_loop.py', 210, 'test_loop_inside_scatter') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_inside_scatter', 'location': ('tests/test_loop.py', 210, 'test_loop_inside_scatter'), 'keywords': {'test_loop_inside_scatter': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003171879998262739, 'start': 1685951439.75998, 'stop': 1685951439.760299, '$report_type': 'TestReport', 'item_index': 436, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_input_deps.py::test_input_deps', 'location': ('tests/test_input_deps.py', 13, 'test_input_deps'), 'keywords': {'test_input_deps': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'")], 'duration': 0.8863417309994475, 'start': 1685951439.006012, 'stop': 1685951439.892333, '$report_type': 'TestReport', 'item_index': 387, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_input_deps.py::test_input_deps', 'location': ('tests/test_input_deps.py', 13, 'test_input_deps'), 'keywords': {'test_input_deps': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'")], 'duration': 0.00023683100062044105, 'start': 1685951439.8928099, 'stop': 1685951439.893048, '$report_type': 'TestReport', 'item_index': 387, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_cmdline_opts', 'location': ('tests/test_input_deps.py', 43, 'test_input_deps_cmdline_opts'), 'keywords': {'test_input_deps_cmdline_opts': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00019443900055193808, 'start': 1685951439.8939362, 'stop': 1685951439.894132, '$report_type': 'TestReport', 'item_index': 388, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_input_deps.py::test_input_deps - location: ('tests/test_input_deps.py', 13, 'test_input_deps') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_input_deps.py::test_input_deps_cmdline_opts - location: ('tests/test_input_deps.py', 43, 'test_input_deps_cmdline_opts') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_when', 'location': ('tests/test_loop.py', 39, 'test_validate_loop_fail_when'), 'keywords': {'test_validate_loop_fail_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-when.cwl:32:11: object id \'tests/loop/invalid-loop-when.cwl#subworkflow/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\n Source is from conditional step and may produce `null`\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-when.cwl:18:3: The `cwltool:Loop` clause is not compatible with the `when`\n directive.\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-when.cwl:32:11: object id \'tests/loop/invalid-loop-when.cwl#subworkflow/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\n Source is from conditional step and may produce `null`\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-when.cwl:18:3: The `cwltool:Loop` clause is not compatible with the `when`\n directive.')], 'duration': 1.040507720000278, 'start': 1685951438.861541, 'stop': 1685951439.902024, '$report_type': 'TestReport', 'item_index': 421, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_when', 'location': ('tests/test_loop.py', 39, 'test_validate_loop_fail_when'), 'keywords': {'test_validate_loop_fail_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-when.cwl:32:11: object id \'tests/loop/invalid-loop-when.cwl#subworkflow/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\n Source is from conditional step and may produce `null`\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-when.cwl:18:3: The `cwltool:Loop` clause is not compatible with the `when`\n directive.\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-when.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-when.cwl:32:11: object id \'tests/loop/invalid-loop-when.cwl#subworkflow/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\n Source is from conditional step and may produce `null`\ntests/loop/invalid-loop-when.cwl:38:11: Source \'o1\' of type ["null", "int"] may be incompatible\ntests/loop/invalid-loop-when.cwl:15:5: with sink \'o1\' of type "int"\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-when.cwl:18:3: The `cwltool:Loop` clause is not compatible with the `when`\n directive.')], 'duration': 0.00021948999983578688, 'start': 1685951439.902556, 'stop': 1685951439.9027772, '$report_type': 'TestReport', 'item_index': 421, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_no_loop_when', 'location': ('tests/test_loop.py', 49, 'test_validate_loop_fail_no_loop_when'), 'keywords': {'test_validate_loop_fail_no_loop_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002804380001180107, 'start': 1685951439.9037492, 'stop': 1685951439.904031, '$report_type': 'TestReport', 'item_index': 422, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_validate_loop_fail_no_loop_when - location: ('tests/test_loop.py', 49, 'test_validate_loop_fail_no_loop_when') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] -ut staging directory /private/tmp/docker_tmp1yceosyd -DEBUG cwltool:job.py:454 [job env.cwl_3] Removing temporary directory /private/tmp/docker_tmpgnhzumjf -DEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/do pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_default_value_loop', 'location': ('tests/test_loop.py', 272, 'test_default_value_loop'), 'keywords': {'test_default_value_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/default-value-loop.cwl:42:7: object id \'tests/loop/default-value-loop.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is used but only a single input source is\n declared\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _2] start\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step loop_2\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step big_values_2\n\x1b[1;30mINFO\x1b[0m [step big_values_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step big_values_3\n\x1b[1;30mINFO\x1b[0m [step big_values_3] start\n\x1b[1;30mINFO\x1b[0m [step big_values_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step big_values_4\n\x1b[1;30mINFO\x1b[0m [step big_values_4] start\n\x1b[1;30mINFO\x1b[0m [step big_values_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step big_values_5\n\x1b[1;30mINFO\x1b[0m [step big_values_5] start\n\x1b[1;30mINFO\x1b[0m [step big_values_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step big_values_6\n\x1b[1;30mINFO\x1b[0m [step big_values_6] start\n\x1b[1;30mINFO\x1b[0m [step big_values_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step big_values_7\n\x1b[1;30mINFO\x1b[0m [step big_values_7] start\n\x1b[1;30mINFO\x1b[0m [step big_values_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/default-value-loop.cwl:42:7: object id \'tests/loop/default-value-loop.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is used but only a single input source is\n declared\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step loop_2\nDEBUG cwltool:workflow_job.py:727 [step loop_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_2] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_2] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step big_values_2\nDEBUG cwltool:workflow_job.py:727 [step big_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_2] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_2] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_2] outputs {\n "o1": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_3] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_3] inputs {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step big_values_3\nDEBUG cwltool:workflow_job.py:727 [step big_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 5\n}\nINFO cwltool:workflow_job.py:75 [step big_values_3] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 8\n}\nINFO cwltool:workflow_job.py:572 [step big_values_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_3] outputs {\n "o1": 8\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_4] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_4] inputs {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step big_values_4\nDEBUG cwltool:workflow_job.py:727 [step big_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 8\n}\nINFO cwltool:workflow_job.py:75 [step big_values_4] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 11\n}\nINFO cwltool:workflow_job.py:572 [step big_values_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_4] outputs {\n "o1": 11\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 11\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_5] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_5] inputs {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step big_values_5\nDEBUG cwltool:workflow_job.py:727 [step big_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 11\n}\nINFO cwltool:workflow_job.py:75 [step big_values_5] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 14\n}\nINFO cwltool:workflow_job.py:572 [step big_values_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_5] outputs {\n "o1": 14\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 14\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_6] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_6] inputs {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step big_values_6\nDEBUG cwltool:workflow_job.py:727 [step big_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 14\n}\nINFO cwltool:workflow_job.py:75 [step big_values_6] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 17\n}\nINFO cwltool:workflow_job.py:572 [step big_values_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_6] outputs {\n "o1": 17\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 17\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_7] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_7] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_7] inputs {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step big_values_7\nDEBUG cwltool:workflow_job.py:727 [step big_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 17\n}\nINFO cwltool:workflow_job.py:75 [step big_values_7] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 20\n}\nINFO cwltool:workflow_job.py:572 [step big_values_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_7] outputs {\n "o1": 20\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 20\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 6 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop_2] loop condition $(inputs.i1 < 20) evaluated to False at iteration 6\nDEBUG cwltool:workflow_job.py:925 [step loop_2] inputs was {\n "i1": 20\n}\nDEBUG cwltool:workflow_job.py:564 [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": [\n null,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {\n "o1": [\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpoar6z8_e\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2uugk7_4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpgertiuxv\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr7t2byqk\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwr14e3q7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo4__2eh4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5y1ls9r3\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1016340950000085, 'start': 1685951439.114841, 'stop': 1685951440.216449, '$report_type': 'TestReport', 'item_index': 441, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_default_value_loop', 'location': ('tests/test_loop.py', 272, 'test_default_value_loop'), 'keywords': {'test_default_value_loop': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/default-value-loop.cwl:42:7: object id \'tests/loop/default-value-loop.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is used but only a single input source is\n declared\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _2] start\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step loop_2\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step big_values_2\n\x1b[1;30mINFO\x1b[0m [step big_values_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step big_values_3\n\x1b[1;30mINFO\x1b[0m [step big_values_3] start\n\x1b[1;30mINFO\x1b[0m [step big_values_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step big_values_4\n\x1b[1;30mINFO\x1b[0m [step big_values_4] start\n\x1b[1;30mINFO\x1b[0m [step big_values_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step big_values_5\n\x1b[1;30mINFO\x1b[0m [step big_values_5] start\n\x1b[1;30mINFO\x1b[0m [step big_values_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step big_values_6\n\x1b[1;30mINFO\x1b[0m [step big_values_6] start\n\x1b[1;30mINFO\x1b[0m [step big_values_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step big_values_7\n\x1b[1;30mINFO\x1b[0m [step big_values_7] start\n\x1b[1;30mINFO\x1b[0m [step big_values_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/default-value-loop.cwl:42:7: object id \'tests/loop/default-value-loop.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is used but only a single input source is\n declared\ntests/loop/default-value-loop.cwl:43:12: Source \'o1\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/default-value-loop.cwl:14:5: with sink \'o1\' of type {"type": "array", "items":\n "int"}\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step loop_2\nDEBUG cwltool:workflow_job.py:727 [step loop_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_2] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_2] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step big_values_2\nDEBUG cwltool:workflow_job.py:727 [step big_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_2] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_2] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_2] outputs {\n "o1": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_3] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_3] inputs {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step big_values_3\nDEBUG cwltool:workflow_job.py:727 [step big_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 5\n}\nINFO cwltool:workflow_job.py:75 [step big_values_3] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 8\n}\nINFO cwltool:workflow_job.py:572 [step big_values_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_3] outputs {\n "o1": 8\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_4] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_4] inputs {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step big_values_4\nDEBUG cwltool:workflow_job.py:727 [step big_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 8\n}\nINFO cwltool:workflow_job.py:75 [step big_values_4] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 11\n}\nINFO cwltool:workflow_job.py:572 [step big_values_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_4] outputs {\n "o1": 11\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 11\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_5] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_5] inputs {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step big_values_5\nDEBUG cwltool:workflow_job.py:727 [step big_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 11\n}\nINFO cwltool:workflow_job.py:75 [step big_values_5] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 14\n}\nINFO cwltool:workflow_job.py:572 [step big_values_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_5] outputs {\n "o1": 14\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 14\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_6] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_6] inputs {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step big_values_6\nDEBUG cwltool:workflow_job.py:727 [step big_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 14\n}\nINFO cwltool:workflow_job.py:75 [step big_values_6] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 17\n}\nINFO cwltool:workflow_job.py:572 [step big_values_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_6] outputs {\n "o1": 17\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 17\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step loop_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_7] initialized from _:022aa143-a788-4727-b73e-415757085424\nINFO cwltool:workflow_job.py:765 [workflow loop_7] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_7] inputs {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step big_values_7\nDEBUG cwltool:workflow_job.py:727 [step big_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/i1": 17\n}\nINFO cwltool:workflow_job.py:75 [step big_values_7] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/run/big_values/o1": 20\n}\nINFO cwltool:workflow_job.py:572 [step big_values_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_7] outputs {\n "o1": 20\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": 20\n}\nINFO cwltool:workflow_job.py:1005 [step loop_2] Iteration 6 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop_2] loop condition $(inputs.i1 < 20) evaluated to False at iteration 6\nDEBUG cwltool:workflow_job.py:925 [step loop_2] inputs was {\n "i1": 20\n}\nDEBUG cwltool:workflow_job.py:564 [step loop_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/default-value-loop.cwl#loop/o1": [\n null,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {\n "o1": [\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpoar6z8_e\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2uugk7_4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpgertiuxv\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr7t2byqk\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwr14e3q7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo4__2eh4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5y1ls9r3\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00047727000037411926, 'start': 1685951440.2176561, 'stop': 1685951440.218135, '$report_type': 'TestReport', 'item_index': 441, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_make_template.py::test_anonymous_record', 'location': ('tests/test_make_template.py', 7, 'test_anonymous_record'), 'keywords': {'test_anonymous_record': 1, 'test_make_template.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00027614000009634765, 'start': 1685951440.219937, 'stop': 1685951440.2202141, '$report_type': 'TestReport', 'item_index': 442, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_default_value_loop - location: ('tests/test_loop.py', 272, 'test_default_value_loop') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_make_template.py::test_anonymous_record - location: ('tests/test_make_template.py', 7, 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[hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_empty_cmdling', 'location': ('tests/test_misc_cli.py', 21, 'test_empty_cmdling'), 'keywords': {'test_empty_cmdling': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nERROR cwltool:main.py:1037 CWL document required, no input file was provided')], 'duration': 0.00021182300042710267, 'start': 1685951440.270251, 'stop': 1685951440.270464, '$report_type': 'TestReport', 'item_index': 447, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_tool_help', 'location': ('tests/test_misc_cli.py', 28, 'test_tool_help'), 'keywords': {'test_tool_help': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00028088700037187664, 'start': 1685951440.271307, 'stop': 1685951440.27159, '$report_type': 'TestReport', 'item_index': 448, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_misc_cli.py::test_empty_cmdling - location: ('tests/test_misc_cli.py', 21, 'test_empty_cmdling') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_misc_cli.py::test_tool_help - location: ('tests/test_misc_cli.py', 28, 'test_tool_help') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_file_overwrite_without_ext', 'location': ('tests/test_ext.py', 106, 'test_disable_file_overwrite_without_ext'), 'keywords': {'test_disable_file_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl'\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] /private/tmp/docker_tmpbn74w3_i$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpbn74w3_i,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdihp24br,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py,readonly \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpyjmpwq8v/20230605095039-365737.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl",\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value"\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updateval.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updateval.cwl] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "size": 102,\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updateval.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updateval.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job updateval.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updateval.cwl] /private/tmp/docker_tmpbn74w3_i$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpbn74w3_i,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdihp24br,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py,readonly \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpyjmpwq8v/20230605095039-365737.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py \\\n value\nINFO cwltool:job.py:905 [job updateval.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job updateval.cwl] completed success\nDEBUG cwltool:job.py:422 [job updateval.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpbn74w3_i/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job updateval.cwl] Removing input staging directory /private/tmp/docker_tmpysfywzqb\nDEBUG cwltool:job.py:454 [job updateval.cwl] Removing temporary directory /private/tmp/docker_tmpdihp24br\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpbn74w3_i/value to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbn74w3_i\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.741776122000374, 'start': 1685951438.650143, 'stop': 1685951440.3918788, '$report_type': 'TestReport', 'item_index': 370, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_file_overwrite_without_ext', 'location': ('tests/test_ext.py', 106, 'test_disable_file_overwrite_without_ext'), 'keywords': {'test_disable_file_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl'\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] /private/tmp/docker_tmpbn74w3_i$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpbn74w3_i,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdihp24br,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py,readonly \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpyjmpwq8v/20230605095039-365737.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job updateval.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl",\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value"\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updateval.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updateval.cwl] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "size": 102,\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updateval.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updateval.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job updateval.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updateval.cwl] /private/tmp/docker_tmpbn74w3_i$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpbn74w3_i,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmpdihp24br,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py,readonly \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpyjmpwq8v/20230605095039-365737.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgadd32212-5041-4601-b165-c9f27c2237c9/updateval.py \\\n value\nINFO cwltool:job.py:905 [job updateval.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job updateval.cwl] completed success\nDEBUG cwltool:job.py:422 [job updateval.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpbn74w3_i/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job updateval.cwl] Removing input staging directory /private/tmp/docker_tmpysfywzqb\nDEBUG cwltool:job.py:454 [job updateval.cwl] Removing temporary directory /private/tmp/docker_tmpdihp24br\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpbn74w3_i/value to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_overwrite_wi0/out/value\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbn74w3_i\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008024259996091132, 'start': 1685951440.393035, 'stop': 1685951440.3938391, '$report_type': 'TestReport', 'item_index': 370, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_disable_file_overwrite_without_ext - location: ('tests/test_ext.py', 106, 'test_disable_file_overwrite_without_ext') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_ext.py::test_disable_dir_overwrite_without_ext - location: ('tests/test_ext.py', 142, 'test_disable_dir_overwrite_without_ext') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_dir_overwrite_without_ext', 'location': ('tests/test_ext.py', 142, 'test_disable_dir_overwrite_without_ext'), 'keywords': {'test_disable_dir_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0019440989999566227, 'start': 1685951440.3958342, 'stop': 1685951440.39778, '$report_type': 'TestReport', 'item_index': 371, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel --debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel --debug]'), 'keywords': {'test_cache_relative_paths[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_7] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_7] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_7] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_7] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmppgt8gdo1/stg66bad48d-a7d9-4436-b9e8-a77b91febaac/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmppgt8gdo1/stg66bad48d-a7d9-4436-b9e8-a77b91febaac/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(secondary-files.cwl_7), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job secondary-files.cwl_7] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_7] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_7] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_7] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_7] Removing input staging directory /private/tmp/docker_tmppgt8gdo1\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_7] Removing temporary directory /private/tmp/docker_tmp9xbgk171\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cacheja0eo8kh\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_8] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_8] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache1e8ss_pv\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.110423813000125, 'start': 1685951438.560262, 'stop': 1685951440.670636, '$report_type': 'TestReport', 'item_index': 303, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cache_relative_paths[--parallel --debug]', 'location': ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel --debug]'), 'keywords': {'test_cache_relative_paths[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_7] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:933 [job secondary-files.cwl_7] Output of job will be cached in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:command_line_tool.py:982 [job secondary-files.cwl_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\nDEBUG cwltool:command_line_tool.py:988 [job secondary-files.cwl_7] {\n "fasta_path": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "size": 671,\n "basename": "2.fasta",\n "nameroot": "2",\n "nameext": ".fasta",\n "secondaryFiles": [\n {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "basename": "2.fastq",\n "class": "File",\n "nameroot": "2",\n "nameext": ".fastq"\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job secondary-files.cwl_7] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fasta": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fasta",\n "/private/tmp/docker_tmppgt8gdo1/stg66bad48d-a7d9-4436-b9e8-a77b91febaac/2.fasta",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/2.fastq": [\n "/Users/jasperk/gitlab/cwltool/tests/2.fastq",\n "/private/tmp/docker_tmppgt8gdo1/stg66bad48d-a7d9-4436-b9e8-a77b91febaac/2.fastq",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job secondary-files.cwl_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(secondary-files.cwl_7), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job secondary-files.cwl_7] initial work dir {}\nINFO cwltool:job.py:266 [job secondary-files.cwl_7] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf$ /bin/sh \\\n -c \\\n ls > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job secondary-files.cwl_7] completed success\nDEBUG cwltool:job.py:422 [job secondary-files.cwl_7] outputs {\n "bai_list": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout",\n "basename": "lsout",\n "nameroot": "lsout",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$12250351818015ffb4ab9ab4efb67c708637b4a7",\n "size": 6,\n "secondaryFiles": [],\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job secondary-files.cwl_7] Removing input staging directory /private/tmp/docker_tmppgt8gdo1\nDEBUG cwltool:job.py:454 [job secondary-files.cwl_7] Removing temporary directory /private/tmp/docker_tmp9xbgk171\nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/out/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cacheja0eo8kh\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/secondary-files.cwl\'\nDEBUG cwltool:command_line_tool.py:903 [job secondary-files.cwl_8] keydictstr is {"2.fasta":[671,"sha1$447f1a92f4863d0b39047d750df67888a4ea7db9"],"2.fastq":[255,"sha1$32b56c80dc3e11da0ed1bc8c639cbb42e36fc541"],"ShellCommandRequirement":{"class":"ShellCommandRequirement"},"cmdline":["ls"],"stdout":"lsout"} -> 27903451fc1ee10c148a0bdeb845b2cf\nINFO cwltool:command_line_tool.py:927 [job secondary-files.cwl_8] Using cached output in /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:process.py:356 Copying /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache/27903451fc1ee10c148a0bdeb845b2cf/lsout to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/out2/lsout\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_cache_relative_paths___pa1/cwltool_cache1e8ss_pv\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0009610970000721863, 'start': 1685951440.6720278, 'stop': 1685951440.672991, '$report_type': 'TestReport', 'item_index': 303, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cache_relative_paths[--parallel --debug] - location: ('tests/test_examples.py', 1282, 'test_cache_relative_paths[--parallel --debug]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_write_summary - location: ('tests/test_examples.py', 1326, 'test_write_summary') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_write_summary', 'location': ('tests/test_examples.py', 1326, 'test_write_summary'), 'keywords': {'test_write_summary': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0024757220007813885, 'start': 1685951440.675128, 'stop': 1685951440.6776068, '$report_type': 'TestReport', 'item_index': 304, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_cmdline_opts', 'location': ('tests/test_input_deps.py', 43, 'test_input_deps_cmdline_opts'), 'keywords': {'test_input_deps_cmdline_opts': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}')], 'duration': 0.8830137269997067, 'start': 1685951439.894478, 'stop': 1685951440.777471, '$report_type': 'TestReport', 'item_index': 388, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_cmdline_opts', 'location': ('tests/test_input_deps.py', 43, 'test_input_deps_cmdline_opts'), 'keywords': {'test_input_deps_cmdline_opts': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}')], 'duration': 0.00019988900021417066, 'start': 1685951440.7779331, 'stop': 1685951440.778133, '$report_type': 'TestReport', 'item_index': 388, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_input_deps.py::test_input_deps_cmdline_opts - location: ('tests/test_input_deps.py', 43, 'test_input_deps_cmdline_opts') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 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report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_no_loop_when', 'location': ('tests/test_loop.py', 49, 'test_validate_loop_fail_no_loop_when'), 'keywords': {'test_validate_loop_fail_no_loop_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-no-loopWhen.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-no-loopWhen.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-no-loopWhen.cwl:31:11: 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pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_misc_cli.py::test_tool_help - location: ('tests/test_misc_cli.py', 28, 'test_tool_help') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_misc_cli.py::test_basic_pack - location: ('tests/test_misc_cli.py', 35, 'test_basic_pack') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_basic_pack', 'location': ('tests/test_misc_cli.py', 35, 'test_basic_pack'), 'keywords': {'test_basic_pack': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 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stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/loop-inside-scatter.cwl:40:13: object id 'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1' previously defined\ntests/loop/loop-inside-scatter.cwl:40:13: object id 'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _10] start\n\x1b[1;30mINFO\x1b[0m [workflow _10] starting step scatter\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter] starting step subworkflow_5\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m 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success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_2] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] starting step subworkflow_7\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] starting step subworkflow_8\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] starting step subworkflow_9\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _10] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-scatter.cwl:40:13: object id \'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-scatter.cwl:40:13: object id \'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {\n "i1": [\n 1,\n 2,\n 3,\n 4,\n 5\n ],\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step scatter\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter] starting step subworkflow_5\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_5] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_5] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_2] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_2] inputs {\n "i1": 2,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_2] starting step subworkflow_6\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 8 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_6] loop condition $(inputs.i1 < 10) evaluated to False at iteration 8\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_6] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_2] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_3] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_3] inputs {\n "i1": 3,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_3] starting step subworkflow_7\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 7 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_7] loop condition $(inputs.i1 < 10) evaluated to False at iteration 7\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_7] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_3] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_4] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_4] inputs {\n "i1": 4,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_4] starting step subworkflow_8\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_8] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 6 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_8] loop condition $(inputs.i1 < 10) evaluated to False at iteration 6\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_8] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_8] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_4] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_5] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_5] inputs {\n "i1": 5,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_5] starting step subworkflow_9\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 5 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_9] loop condition $(inputs.i1 < 10) evaluated to False at iteration 5\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_9] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_9] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_5] outputs {\n "o1": 10\n}\nDEBUG cwltool:workflow_job.py:564 [step scatter] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/o1": [\n 10,\n 10,\n 10,\n 10,\n 10\n ]\n}\nINFO cwltool:workflow_job.py:572 [step scatter] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {\n "o1": [\n 10,\n 10,\n 10,\n 10,\n 10\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3toza5rh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa65hoj0o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp09jo_4c_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1vhvuysq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo6sf1hnz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5og7ngfg\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.3274409570003627, 'start': 1685951439.760791, 'stop': 1685951441.088199, '$report_type': 'TestReport', 'item_index': 436, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_inside_scatter', 'location': ('tests/test_loop.py', 210, 'test_loop_inside_scatter'), 'keywords': {'test_loop_inside_scatter': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/loop-inside-scatter.cwl:40:13: object id 'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1' previously defined\ntests/loop/loop-inside-scatter.cwl:40:13: object id 'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _10] start\n\x1b[1;30mINFO\x1b[0m [workflow _10] starting step scatter\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter] starting step subworkflow_5\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_2] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_2] starting step subworkflow_6\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_2] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] starting step subworkflow_7\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_3] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] starting step subworkflow_8\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_8] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_4] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] start\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] starting step subworkflow_9\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_9] completed success\n\x1b[1;30mINFO\x1b[0m [workflow scatter_5] completed success\n\x1b[1;30mINFO\x1b[0m [step scatter] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _10] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-scatter.cwl:40:13: object id \'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-scatter.cwl:40:13: object id \'tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {\n "i1": [\n 1,\n 2,\n 3,\n 4,\n 5\n ],\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step scatter\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter] starting step subworkflow_5\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_5] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_5] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_2] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_2] inputs {\n "i1": 2,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_2] starting step subworkflow_6\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_6] Iteration 8 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_6] loop condition $(inputs.i1 < 10) evaluated to False at iteration 8\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_6] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_2] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_3] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_3] inputs {\n "i1": 3,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_3] starting step subworkflow_7\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_7] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_7] Iteration 7 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_7] loop condition $(inputs.i1 < 10) evaluated to False at iteration 7\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_7] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_3] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_4] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_4] inputs {\n "i1": 4,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_4] starting step subworkflow_8\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_8] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_8] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_8] Iteration 6 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_8] loop condition $(inputs.i1 < 10) evaluated to False at iteration 6\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_8] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_8] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_4] outputs {\n "o1": 10\n}\nINFO cwltool:workflow_job.py:75 [step scatter] start\nDEBUG cwltool:workflow_job.py:498 [workflow scatter_5] initialized from _:6c131362-87d2-402b-b1c5-d7e3cfb27e70\nINFO cwltool:workflow_job.py:765 [workflow scatter_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow scatter_5] inputs {\n "i1": 5,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow scatter_5] starting step subworkflow_9\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_9] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_9] Iteration 5 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_9] loop condition $(inputs.i1 < 10) evaluated to False at iteration 5\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_9] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/run/subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_9] completed success\nINFO cwltool:workflow_job.py:539 [workflow scatter_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow scatter_5] outputs {\n "o1": 10\n}\nDEBUG cwltool:workflow_job.py:564 [step scatter] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-scatter.cwl#scatter/o1": [\n 10,\n 10,\n 10,\n 10,\n 10\n ]\n}\nINFO cwltool:workflow_job.py:572 [step scatter] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {\n "o1": [\n 10,\n 10,\n 10,\n 10,\n 10\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3toza5rh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa65hoj0o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp09jo_4c_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1vhvuysq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo6sf1hnz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5og7ngfg\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006262719998630928, 'start': 1685951441.089491, 'stop': 1685951441.090119, '$report_type': 'TestReport', 'item_index': 436, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_nested_loops', 'location': ('tests/test_loop.py', 223, 'test_nested_loops'), 'keywords': {'test_nested_loops': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00025334400015708525, 'start': 1685951441.091902, 'stop': 1685951441.092157, '$report_type': 'TestReport', 'item_index': 437, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_loop_inside_scatter - location: ('tests/test_loop.py', 210, 'test_loop_inside_scatter') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_nested_loops - location: ('tests/test_loop.py', 223, 'test_nested_loops') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]'), 'keywords': {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task1_10\nDEBUG cwltool:workflow_job.py:727 [step task1_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_10\nDEBUG cwltool:command_line_tool.py:988 [job task1_8] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_8] initial work dir {}\nINFO cwltool:job.py:266 [job task1_8] /private/tmp/docker_tmpqd0zbt01$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqd0zbt01,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwbwvw4vq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095039-089090.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_8] completed success\nDEBUG cwltool:job.py:422 [job task1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqd0zbt01/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_10] completed success\nDEBUG cwltool:job.py:446 [job task1_8] Removing input staging directory /private/tmp/docker_tmpsuq2jbza\nDEBUG cwltool:job.py:454 [job task1_8] Removing temporary directory /private/tmp/docker_tmpwbwvw4vq\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task2_10\nDEBUG cwltool:workflow_job.py:727 [step task2_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_10\nDEBUG cwltool:command_line_tool.py:988 [job task2_8] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_8] initial work dir {}\nINFO cwltool:job.py:266 [job task2_8] /private/tmp/docker_tmpukxzzulb$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpukxzzulb,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp460y3fko,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095040-128027.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_8] completed success\nDEBUG cwltool:job.py:422 [job task2_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpukxzzulb/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_10] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {}\nDEBUG cwltool:job.py:446 [job task2_8] Removing input staging directory /private/tmp/docker_tmp0ewn2kda\nDEBUG cwltool:job.py:454 [job task2_8] Removing temporary directory /private/tmp/docker_tmp460y3fko\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpukxzzulb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqd0zbt01\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6qs7k1_4\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 3.6632841119999284, 'start': 1685951437.4933639, 'stop': 1685951441.156561, '$report_type': 'TestReport', 'item_index': 276, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]'), 'keywords': {'test_cid_file_w_prefix[]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _10] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _10] start\nDEBUG cwltool:workflow_job.py:777 [workflow _10] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task1_10\nDEBUG cwltool:workflow_job.py:727 [step task1_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_10\nDEBUG cwltool:command_line_tool.py:988 [job task1_8] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_8] initial work dir {}\nINFO cwltool:job.py:266 [job task1_8] /private/tmp/docker_tmpqd0zbt01$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqd0zbt01,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwbwvw4vq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095039-089090.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_8] completed success\nDEBUG cwltool:job.py:422 [job task1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqd0zbt01/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_10] completed success\nDEBUG cwltool:job.py:446 [job task1_8] Removing input staging directory /private/tmp/docker_tmpsuq2jbza\nDEBUG cwltool:job.py:454 [job task1_8] Removing temporary directory /private/tmp/docker_tmpwbwvw4vq\nINFO cwltool:workflow_job.py:613 [workflow _10] starting step task2_10\nDEBUG cwltool:workflow_job.py:727 [step task2_10] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_10] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_10] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_10\nDEBUG cwltool:command_line_tool.py:988 [job task2_8] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_8] initial work dir {}\nINFO cwltool:job.py:266 [job task2_8] /private/tmp/docker_tmpukxzzulb$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpukxzzulb,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp460y3fko,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix__0/pytestcid-20230605095040-128027.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_8] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_8] completed success\nDEBUG cwltool:job.py:422 [job task2_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpukxzzulb/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_10] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_10] completed success\nINFO cwltool:workflow_job.py:539 [workflow _10] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _10] outputs {}\nDEBUG cwltool:job.py:446 [job task2_8] Removing input staging directory /private/tmp/docker_tmp0ewn2kda\nDEBUG cwltool:job.py:454 [job task2_8] Removing temporary directory /private/tmp/docker_tmp460y3fko\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpukxzzulb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqd0zbt01\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6qs7k1_4\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008422430000791792, 'start': 1685951441.1581, 'stop': 1685951441.158945, '$report_type': 'TestReport', 'item_index': 276, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]'), 'keywords': {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0020675499999924796, 'start': 1685951441.160426, 'stop': 1685951441.162495, '$report_type': 'TestReport', 'item_index': 277, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_dir_overwrite_without_ext', 'location': ('tests/test_ext.py', 142, 'test_disable_dir_overwrite_without_ext'), 'keywords': {'test_disable_dir_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp",\n "basename": "inp",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp/blurb",\n "basename": "blurb",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp/blurb"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl'\n\x1b[1;30mINFO\x1b[0m [job updatedir.cwl] /private/tmp/docker_tmp9bw9d8xw$ touch \\\n inp/blurb\n\x1b[1;30mINFO\x1b[0m [job updatedir.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl",\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updatedir.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updatedir.cwl] {\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "basename": "tmp",\n "listing": []\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updatedir.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "/private/tmp/docker_tmp9bw9d8xw/inp",\n "WritableDirectory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updatedir.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp/blurb"\n }\n]\nDEBUG cwltool:job.py:215 [job updatedir.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "/private/tmp/docker_tmp9bw9d8xw/inp",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updatedir.cwl] /private/tmp/docker_tmp9bw9d8xw$ touch \\\n inp/blurb\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job updatedir.cwl] completed success\nDEBUG cwltool:job.py:422 [job updatedir.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9bw9d8xw/inp",\n "basename": "inp",\n "nameroot": "inp",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job updatedir.cwl] Removing input staging directory /private/tmp/docker_tmpg93e0s32\nDEBUG cwltool:job.py:454 [job updatedir.cwl] Removing temporary directory /private/tmp/docker_tmp6xesz114\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp9bw9d8xw/inp to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9bw9d8xw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7997955589999037, 'start': 1685951440.398328, 'stop': 1685951441.198105, '$report_type': 'TestReport', 'item_index': 371, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_dir_overwrite_without_ext', 'location': ('tests/test_ext.py', 142, 'test_disable_dir_overwrite_without_ext'), 'keywords': {'test_disable_dir_overwrite_without_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp",\n "basename": "inp",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp/blurb",\n "basename": "blurb",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp/blurb"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl'\n\x1b[1;30mINFO\x1b[0m [job updatedir.cwl] /private/tmp/docker_tmp9bw9d8xw$ touch \\\n inp/blurb\n\x1b[1;30mINFO\x1b[0m [job updatedir.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl",\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updatedir.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updatedir.cwl] {\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "basename": "tmp",\n "listing": []\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updatedir.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "/private/tmp/docker_tmp9bw9d8xw/inp",\n "WritableDirectory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updatedir.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp/blurb"\n }\n]\nDEBUG cwltool:job.py:215 [job updatedir.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/tmp",\n "/private/tmp/docker_tmp9bw9d8xw/inp",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updatedir.cwl] /private/tmp/docker_tmp9bw9d8xw$ touch \\\n inp/blurb\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job updatedir.cwl] completed success\nDEBUG cwltool:job.py:422 [job updatedir.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9bw9d8xw/inp",\n "basename": "inp",\n "nameroot": "inp",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job updatedir.cwl] Removing input staging directory /private/tmp/docker_tmpg93e0s32\nDEBUG cwltool:job.py:454 [job updatedir.cwl] Removing temporary directory /private/tmp/docker_tmp6xesz114\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp9bw9d8xw/inp to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_overwrite_wit0/outdir/inp\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9bw9d8xw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007611159999214578, 'start': 1685951441.199606, 'stop': 1685951441.200369, '$report_type': 'TestReport', 'item_index': 371, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_disable_dir_overwrite_without_ext - location: ('tests/test_ext.py', 142, 'test_disable_dir_overwrite_without_ext') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_ext.py::test_disable_file_creation_in_outdir_with_ext - location: ('tests/test_ext.py', 155, 'test_disable_file_creation_in_outdir_with_ext') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_file_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 155, 'test_disable_file_creation_in_outdir_with_ext'), 'keywords': {'test_disable_file_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013144630001988844, 'start': 1685951441.2017689, 'stop': 1685951441.203084, '$report_type': 'TestReport', 'item_index': 372, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_cmdline_opts_relative_deps_cwd', 'location': ('tests/test_input_deps.py', 73, 'test_input_deps_cmdline_opts_relative_deps_cwd'), 'keywords': {'test_input_deps_cmdline_opts_relative_deps_cwd': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}')], 'duration': 0.7899493630002326, 'start': 1685951440.779573, 'stop': 1685951441.569504, '$report_type': 'TestReport', 'item_index': 389, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_cmdline_opts_relative_deps_cwd', 'location': ('tests/test_input_deps.py', 73, 'test_input_deps_cmdline_opts_relative_deps_cwd'), 'keywords': {'test_input_deps_cmdline_opts_relative_deps_cwd': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}')], 'duration': 0.00020822599981329404, 'start': 1685951441.5699599, 'stop': 1685951441.570169, '$report_type': 'TestReport', 'item_index': 389, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_secondary_files', 'location': ('tests/test_input_deps.py', 107, 'test_input_deps_secondary_files'), 'keywords': {'test_input_deps_secondary_files': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00023992099977476755, 'start': 1685951441.571033, 'stop': 1685951441.571274, '$report_type': 'TestReport', 'item_index': 390, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_input_deps.py::test_input_deps_cmdline_opts_relative_deps_cwd - location: ('tests/test_input_deps.py', 73, 'test_input_deps_cmdline_opts_relative_deps_cwd') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_input_deps.py::test_input_deps_secondary_files - location: ('tests/test_input_deps.py', 107, 'test_input_deps_secondary_files') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_basic_pack', 'location': ('tests/test_misc_cli.py', 35, 'test_basic_pack'), 'keywords': {'test_basic_pack': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'")], 'duration': 0.7982027429998197, 'start': 1685951441.066327, 'stop': 1685951441.864511, '$report_type': 'TestReport', 'item_index': 449, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - 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section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-workflow.cwl:13:7: object id 'tests/loop/invalid-loop-workflow.cwl#i1' previously defined\nERROR cwltool:main.py:1211 Tool definition failed initialization:\ntests/loop/invalid-loop-workflow.cwl:10:3: Unsupported requirement http://commonwl.org/cwltool#Loop.")], 'duration': 0.9319351900003312, 'start': 1685951440.9462762, 'stop': 1685951441.878189, '$report_type': 'TestReport', 'item_index': 423, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_workflow', 'location': 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'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-workflow.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-workflow.cwl:13:7: object id 'tests/loop/invalid-loop-workflow.cwl#i1' previously defined\nERROR cwltool:main.py:1211 Tool definition failed initialization:\ntests/loop/invalid-loop-workflow.cwl:10:3: Unsupported requirement http://commonwl.org/cwltool#Loop.")], 'duration': 0.00021205800021562027, 'start': 1685951441.8786712, 'stop': 1685951441.878884, '$report_type': 'TestReport', 'item_index': 423, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: 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loop2\n\x1b[1;30mINFO\x1b[0m [step loop2] start\n\x1b[1;30mINFO\x1b[0m [step loop2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] starting step loop2_2\n\x1b[1;30mINFO\x1b[0m [step loop2_2] start\n\x1b[1;30mINFO\x1b[0m [step loop2_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_2] start\n\x1b[1;30mINFO\x1b[0m [step loop2_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] starting step loop2_3\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _11] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:41:13: object id \'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:41:13: object id \'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:52:7: object id \'tests/loop/loop-inside-loop.cwl#loop1/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step loop1\nDEBUG cwltool:workflow_job.py:727 [step loop1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1] starting step loop2\nDEBUG cwltool:workflow_job.py:727 [step loop2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2] Iteration 1 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 1\nDEBUG cwltool:workflow_job.py:925 [step loop2] inputs was {\n "i1": 2,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step loop2] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1] outputs {\n "o1": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_2] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_2] inputs {\n "i1": 1,\n "i2": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_2] starting step loop2_2\nDEBUG cwltool:workflow_job.py:727 [step loop2_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 2\n}\nINFO cwltool:workflow_job.py:75 [step loop2_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_2] Iteration 2 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_2] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 2\nDEBUG cwltool:workflow_job.py:925 [step loop2_2] inputs was {\n "i1": 3,\n "i2": 2\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:572 [step loop2_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_2] outputs {\n "o1": 3\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_3] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_3] inputs {\n "i1": 1,\n "i2": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_3] starting step loop2_3\nDEBUG cwltool:workflow_job.py:727 [step loop2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 3\n}\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_3] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop2_3] inputs was {\n "i1": 4,\n "i2": 3\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:572 [step loop2_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_3] outputs {\n "o1": 4\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop1] loop condition $(inputs.i2 < 4) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop1] inputs was {\n "i1": 1,\n "i2": 4\n}\nDEBUG cwltool:workflow_job.py:564 [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {\n "o1": [\n 2,\n 3,\n 4\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp86kxxkxs\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpx1mswbm8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpicj1_df4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0soc3lb5\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.053414222000356, 'start': 1685951441.092515, 'stop': 1685951442.145904, '$report_type': 'TestReport', 'item_index': 437, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_nested_loops', 'location': ('tests/test_loop.py', 223, 'test_nested_loops'), 'keywords': {'test_nested_loops': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/loop-inside-loop.cwl:41:13: object id 'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop.cwl:41:13: object id 'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop.cwl:52:7: object id 'tests/loop/loop-inside-loop.cwl#loop1/i2' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _11] start\n\x1b[1;30mINFO\x1b[0m [workflow _11] starting step loop1\n\x1b[1;30mINFO\x1b[0m [step loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1] starting step loop2\n\x1b[1;30mINFO\x1b[0m [step loop2] start\n\x1b[1;30mINFO\x1b[0m [step loop2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] starting step loop2_2\n\x1b[1;30mINFO\x1b[0m [step loop2_2] start\n\x1b[1;30mINFO\x1b[0m [step loop2_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_2] start\n\x1b[1;30mINFO\x1b[0m [step loop2_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] starting step loop2_3\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] start\n\x1b[1;30mINFO\x1b[0m [step loop2_3] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _11] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:41:13: object id \'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:41:13: object id \'tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop.cwl:52:7: object id \'tests/loop/loop-inside-loop.cwl#loop1/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step loop1\nDEBUG cwltool:workflow_job.py:727 [step loop1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1] starting step loop2\nDEBUG cwltool:workflow_job.py:727 [step loop2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2] Iteration 1 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 1\nDEBUG cwltool:workflow_job.py:925 [step loop2] inputs was {\n "i1": 2,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step loop2] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1] outputs {\n "o1": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_2] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_2] inputs {\n "i1": 1,\n "i2": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_2] starting step loop2_2\nDEBUG cwltool:workflow_job.py:727 [step loop2_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 2\n}\nINFO cwltool:workflow_job.py:75 [step loop2_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_2] Iteration 2 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_2] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 2\nDEBUG cwltool:workflow_job.py:925 [step loop2_2] inputs was {\n "i1": 3,\n "i2": 2\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:572 [step loop2_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_2] outputs {\n "o1": 3\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop1] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_3] initialized from _:020d2e8b-6109-4657-8e43-0c6ffe4bb4de\nINFO cwltool:workflow_job.py:765 [workflow loop1_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_3] inputs {\n "i1": 1,\n "i2": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_3] starting step loop2_3\nDEBUG cwltool:workflow_job.py:727 [step loop2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/i2": 3\n}\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_3] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_3] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_3] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop2_3] inputs was {\n "i1": 4,\n "i2": 3\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:572 [step loop2_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_3] outputs {\n "o1": 4\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop1] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop1] loop condition $(inputs.i2 < 4) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop1] inputs was {\n "i1": 1,\n "i2": 4\n}\nDEBUG cwltool:workflow_job.py:564 [step loop1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop.cwl#loop1/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {\n "o1": [\n 2,\n 3,\n 4\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp86kxxkxs\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpx1mswbm8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpicj1_df4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0soc3lb5\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00048784200043883175, 'start': 1685951442.147024, 'stop': 1685951442.147514, '$report_type': 'TestReport', 'item_index': 437, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_nested_loops - location: ('tests/test_loop.py', 223, 'test_nested_loops') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_nested_loops_all - location: ('tests/test_loop.py', 236, 'test_nested_loops_all') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_nested_loops_all', 'location': ('tests/test_loop.py', 236, 'test_nested_loops_all'), 'keywords': {'test_nested_loops_all': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000564637000024959, 'start': 1685951442.149386, 'stop': 1685951442.149954, '$report_type': 'TestReport', 'item_index': 438, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_write_summary', 'location': ('tests/test_examples.py', 1326, 'test_write_summary'), 'keywords': {'test_write_summary': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl",\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:982 [job no-parameters-echo.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job no-parameters-echo.cwl] {\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job no-parameters-echo.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job no-parameters-echo.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n }\n]\nDEBUG cwltool:job.py:215 [job no-parameters-echo.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job no-parameters-echo.cwl] /private/tmp/docker_tmp2imu6nl2$ echo > /private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job no-parameters-echo.cwl] completed success\nDEBUG cwltool:job.py:422 [job no-parameters-echo.cwl] outputs {\n "e_out": {\n "location": "file:///private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "basename": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameroot": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job no-parameters-echo.cwl] Removing input staging directory /private/tmp/docker_tmpxbhyjn_4\nDEBUG cwltool:job.py:454 [job no-parameters-echo.cwl] Removing temporary directory /private/tmp/docker_tmpo4kfuhls\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_write_summary0/out1/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2imu6nl2\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl",\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:982 [job no-parameters-echo.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job no-parameters-echo.cwl_2] {\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job no-parameters-echo.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job no-parameters-echo.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n }\n]\nDEBUG cwltool:job.py:215 [job no-parameters-echo.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job no-parameters-echo.cwl_2] /private/tmp/docker_tmpkot0d5xg$ echo > /private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job no-parameters-echo.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job no-parameters-echo.cwl_2] outputs {\n "e_out": {\n "location": "file:///private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "basename": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameroot": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job no-parameters-echo.cwl_2] Removing input staging directory /private/tmp/docker_tmplio_v9ds\nDEBUG cwltool:job.py:454 [job no-parameters-echo.cwl_2] Removing temporary directory /private/tmp/docker_tmpcl153tce\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_write_summary0/out2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkot0d5xg\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.5343125399995188, 'start': 1685951440.678324, 'stop': 1685951442.2126021, '$report_type': 'TestReport', 'item_index': 304, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_write_summary', 'location': ('tests/test_examples.py', 1326, 'test_write_summary'), 'keywords': {'test_write_summary': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl",\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:982 [job no-parameters-echo.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job no-parameters-echo.cwl] {\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job no-parameters-echo.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job no-parameters-echo.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n }\n]\nDEBUG cwltool:job.py:215 [job no-parameters-echo.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job no-parameters-echo.cwl] /private/tmp/docker_tmp2imu6nl2$ echo > /private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job no-parameters-echo.cwl] completed success\nDEBUG cwltool:job.py:422 [job no-parameters-echo.cwl] outputs {\n "e_out": {\n "location": "file:///private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "basename": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameroot": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job no-parameters-echo.cwl] Removing input staging directory /private/tmp/docker_tmpxbhyjn_4\nDEBUG cwltool:job.py:454 [job no-parameters-echo.cwl] Removing temporary directory /private/tmp/docker_tmpo4kfuhls\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp2imu6nl2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_write_summary0/out1/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2imu6nl2\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl",\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:982 [job no-parameters-echo.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/no-parameters-echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job no-parameters-echo.cwl_2] {\n "in": "foo"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job no-parameters-echo.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job no-parameters-echo.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n }\n]\nDEBUG cwltool:job.py:215 [job no-parameters-echo.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job no-parameters-echo.cwl_2] /private/tmp/docker_tmpkot0d5xg$ echo > /private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job no-parameters-echo.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job no-parameters-echo.cwl_2] outputs {\n "e_out": {\n "location": "file:///private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "basename": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameroot": "30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job no-parameters-echo.cwl_2] Removing input staging directory /private/tmp/docker_tmplio_v9ds\nDEBUG cwltool:job.py:454 [job no-parameters-echo.cwl_2] Removing temporary directory /private/tmp/docker_tmpcl153tce\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpkot0d5xg/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_write_summary0/out2/30d1f5a2e94a97ae02d4130dfc2fa34d04a3f121\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkot0d5xg\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007945969991851598, 'start': 1685951442.2140448, 'stop': 1685951442.2148411, '$report_type': 'TestReport', 'item_index': 304, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_write_summary - location: ('tests/test_examples.py', 1326, 'test_write_summary') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_compute_checksum - location: ('tests/test_examples.py', 1355, 'test_compute_checksum') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_compute_checksum', 'location': ('tests/test_examples.py', 1355, 'test_compute_checksum'), 'keywords': {'test_compute_checksum': 1, 'skipif': 1, 'pytestmark': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018198719999418245, 'start': 1685951442.217089, 'stop': 1685951442.21891, '$report_type': 'TestReport', 'item_index': 305, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_compute_checksum', 'location': ('tests/test_examples.py', 1355, 'test_compute_checksum'), 'keywords': {'test_compute_checksum': 1, 'skipif': 1, 'pytestmark': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\'\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n },\n "reverse": false\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m [job cat-tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z$ cat < /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m [job cat-tool.cwl] completed success\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] outputs {\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/kaqzgbml\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_compute_checksum0/output\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job cat-tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job cat-tool.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n },\n "reverse": false\n}\nDEBUG cwltool:command_line_tool.py:1000 [job cat-tool.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job cat-tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n }\n]\nDEBUG cwltool:job.py:215 [job cat-tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job cat-tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z$ cat < /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job cat-tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job cat-tool.cwl] outputs {\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job cat-tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd\nDEBUG cwltool:job.py:454 [job cat-tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/kaqzgbml\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_compute_checksum0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z')], 'duration': 0.04705045799983054, 'start': 1685951442.219559, 'stop': 1685951442.2666109, '$report_type': 'TestReport', 'item_index': 305, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_compute_checksum', 'location': ('tests/test_examples.py', 1355, 'test_compute_checksum'), 'keywords': {'test_compute_checksum': 1, 'skipif': 1, 'pytestmark': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\'\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n },\n "reverse": false\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m [job cat-tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z$ cat < /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m [job cat-tool.cwl] completed success\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] outputs {\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cat-tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/kaqzgbml\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_compute_checksum0/output\x1b[0m\n\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job cat-tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/cat-tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job cat-tool.cwl] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n },\n "reverse": false\n}\nDEBUG cwltool:command_line_tool.py:1000 [job cat-tool.cwl] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job cat-tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n }\n]\nDEBUG cwltool:job.py:215 [job cat-tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job cat-tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z$ cat < /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd/stgab085439-9c82-4f0b-9a21-6eac16ee1642/whale.txt > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job cat-tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job cat-tool.cwl] outputs {\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job cat-tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/enmijxsd\nDEBUG cwltool:job.py:454 [job cat-tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/kaqzgbml\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_compute_checksum0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/vge5sa6z')], 'duration': 0.0006137840000519645, 'start': 1685951442.267637, 'stop': 1685951442.268252, '$report_type': 'TestReport', 'item_index': 305, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_compute_checksum - location: ('tests/test_examples.py', 1355, 'test_compute_checksum') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::TestMpiRun::test_simple_mpi_tool - location: ('tests/test_mpi.py', 137, 'TestMpiRun.test_simple_mpi_tool') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_tool', 'location': ('tests/test_mpi.py', 137, 'TestMpiRun.test_simple_mpi_tool'), 'keywords': {'test_simple_mpi_tool': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.007654691000425373, 'start': 1685951442.270446, 'stop': 1685951442.278104, '$report_type': 'TestReport', 'item_index': 456, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_secondary_files', 'location': ('tests/test_input_deps.py', 107, 'test_input_deps_secondary_files'), 'keywords': {'test_input_deps_secondary_files': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl'")], 'duration': 0.9784087640000507, 'start': 1685951441.571808, 'stop': 1685951442.550194, '$report_type': 'TestReport', 'item_index': 390, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_input_deps.py::test_input_deps_secondary_files', 'location': ('tests/test_input_deps.py', 107, 'test_input_deps_secondary_files'), 'keywords': {'test_input_deps_secondary_files': 1, 'test_input_deps.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/input_deps/docker-array-secondaryfiles.cwl'")], 'duration': 0.00031209000007947907, 'start': 1685951442.55082, 'stop': 1685951442.5511339, '$report_type': 'TestReport', 'item_index': 390, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_input_deps.py::test_input_deps_secondary_files - location: ('tests/test_input_deps.py', 107, 'test_input_deps_secondary_files') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_iwdr.py::test_newline_in_entry - location: ('tests/test_iwdr.py', 15, 'test_newline_in_entry') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_newline_in_entry', 'location': ('tests/test_iwdr.py', 15, 'test_newline_in_entry'), 'keywords': {'test_newline_in_entry': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002904470002249582, 'start': 1685951442.552471, 'stop': 1685951442.552763, '$report_type': 'TestReport', 'item_index': 391, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_basic_print_subgraph', 'location': ('tests/test_misc_cli.py', 42, 'test_basic_print_subgraph'), 'keywords': {'test_basic_print_subgraph': 1, 'skipif': 1, 'pytestmark': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines1-wf.cwl'\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.9936495560004914, 'start': 1685951441.867296, 'stop': 1685951442.8609228, '$report_type': 'TestReport', 'item_index': 450, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_basic_print_subgraph', 'location': ('tests/test_misc_cli.py', 42, 'test_basic_print_subgraph'), 'keywords': {'test_basic_print_subgraph': 1, 'skipif': 1, 'pytestmark': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines1-wf.cwl'\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.0003293109994046972, 'start': 1685951442.8618062, 'stop': 1685951442.862138, '$report_type': 'TestReport', 'item_index': 450, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_misc_cli.py::test_basic_print_subgraph - location: ('tests/test_misc_cli.py', 42, 'test_basic_print_subgraph') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_misc_cli.py::test_error_graph_with_no_default - location: ('tests/test_misc_cli.py', 55, 'test_error_graph_with_no_default') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_error_graph_with_no_default', 'location': ('tests/test_misc_cli.py', 55, 'test_error_graph_with_no_default'), 'keywords': {'test_error_graph_with_no_default': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002873619996535126, 'start': 1685951442.863449, 'stop': 1685951442.863738, '$report_type': 'TestReport', 'item_index': 451, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_command_line_tool', 'location': ('tests/test_loop.py', 69, 'test_validate_loop_fail_on_command_line_tool'), 'keywords': {'test_validate_loop_fail_on_command_line_tool': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-command-line-tool.cwl:11:7: object id 'tests/loop/invalid-loop-command-line-tool.cwl#i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed initialization:\ntests/loop/invalid-loop-command-line-tool.cwl:8:3: Unsupported requirement http://commonwl.org/cwltool#Loop.\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-command-line-tool.cwl:11:7: object id 'tests/loop/invalid-loop-command-line-tool.cwl#i1' previously defined\nERROR cwltool:main.py:1211 Tool definition failed initialization:\ntests/loop/invalid-loop-command-line-tool.cwl:8:3: Unsupported requirement http://commonwl.org/cwltool#Loop.")], 'duration': 1.063583369999833, 'start': 1685951441.880509, 'stop': 1685951442.9440682, '$report_type': 'TestReport', 'item_index': 424, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_command_line_tool', 'location': ('tests/test_loop.py', 69, 'test_validate_loop_fail_on_command_line_tool'), 'keywords': {'test_validate_loop_fail_on_command_line_tool': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-command-line-tool.cwl:11:7: object id 'tests/loop/invalid-loop-command-line-tool.cwl#i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed initialization:\ntests/loop/invalid-loop-command-line-tool.cwl:8:3: Unsupported requirement http://commonwl.org/cwltool#Loop.\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-command-line-tool.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-command-line-tool.cwl:11:7: object id 'tests/loop/invalid-loop-command-line-tool.cwl#i1' previously defined\nERROR cwltool:main.py:1211 Tool definition failed initialization:\ntests/loop/invalid-loop-command-line-tool.cwl:8:3: Unsupported requirement http://commonwl.org/cwltool#Loop.")], 'duration': 0.0002101680001942441, 'start': 1685951442.944543, 'stop': 1685951442.944754, '$report_type': 'TestReport', 'item_index': 424, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_expression_tool', 'location': ('tests/test_loop.py', 79, 'test_validate_loop_fail_on_expression_tool'), 'keywords': {'test_validate_loop_fail_on_expression_tool': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00019860999964294024, 'start': 1685951442.945764, 'stop': 1685951442.945964, '$report_type': 'TestReport', 'item_index': 425, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_validate_loop_fail_on_command_line_tool - location: ('tests/test_loop.py', 69, 'test_validate_loop_fail_on_command_line_tool') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_validate_loop_fail_on_expression_tool - location: ('tests/test_loop.py', 79, 'test_validate_loop_fail_on_expression_tool') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_file_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 155, 'test_disable_file_creation_in_outdir_with_ext'), 'keywords': {'test_disable_file_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmpxknywf47/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "path": "/private/tmp/docker_tmpxknywf47/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl'\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] /private/tmp/docker_tmpxknywf47$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpxknywf47,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp9frq7sxn,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpjuxvtp7d/20230605095042-024812.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl",\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value"\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updateval_inplace.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updateval_inplace.cwl] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "size": 102,\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updateval_inplace.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updateval_inplace.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job updateval_inplace.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updateval_inplace.cwl] /private/tmp/docker_tmpxknywf47$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpxknywf47,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp9frq7sxn,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpjuxvtp7d/20230605095042-024812.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py \\\n value\nINFO cwltool:job.py:905 [job updateval_inplace.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job updateval_inplace.cwl] completed success\nDEBUG cwltool:job.py:422 [job updateval_inplace.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxknywf47/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job updateval_inplace.cwl] Removing input staging directory /private/tmp/docker_tmpju1om5_7\nDEBUG cwltool:job.py:454 [job updateval_inplace.cwl] Removing temporary directory /private/tmp/docker_tmp9frq7sxn\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxknywf47\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.8482773919995452, 'start': 1685951441.2034738, 'stop': 1685951443.0517068, '$report_type': 'TestReport', 'item_index': 372, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_file_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 155, 'test_disable_file_creation_in_outdir_with_ext'), 'keywords': {'test_disable_file_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmpxknywf47/value",\n "basename": "value",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "path": "/private/tmp/docker_tmpxknywf47/value"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl'\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] /private/tmp/docker_tmpxknywf47$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpxknywf47,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp9frq7sxn,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpjuxvtp7d/20230605095042-024812.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job updateval_inplace.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl",\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value"\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updateval_inplace.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updateval_inplace.cwl] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "size": 102,\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updateval_inplace.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updateval_inplace.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job updateval_inplace.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updateval_inplace.cwl] /private/tmp/docker_tmpxknywf47$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpxknywf47,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp9frq7sxn,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_file_creation_in_0/tmp/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpjuxvtp7d/20230605095042-024812.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stgcee0c68d-8f38-46f8-8c4b-3618288d6005/updateval.py \\\n value\nINFO cwltool:job.py:905 [job updateval_inplace.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job updateval_inplace.cwl] completed success\nDEBUG cwltool:job.py:422 [job updateval_inplace.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxknywf47/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job updateval_inplace.cwl] Removing input staging directory /private/tmp/docker_tmpju1om5_7\nDEBUG cwltool:job.py:454 [job updateval_inplace.cwl] Removing temporary directory /private/tmp/docker_tmp9frq7sxn\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxknywf47\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008131670001603197, 'start': 1685951443.053161, 'stop': 1685951443.053976, '$report_type': 'TestReport', 'item_index': 372, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_disable_file_creation_in_outdir_with_ext - location: ('tests/test_ext.py', 155, 'test_disable_file_creation_in_outdir_with_ext') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_ext.py::test_disable_dir_creation_in_outdir_with_ext - location: ('tests/test_ext.py', 186, 'test_disable_dir_creation_in_outdir_with_ext') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_dir_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 186, 'test_disable_dir_creation_in_outdir_with_ext'), 'keywords': {'test_disable_dir_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0028105779992984026, 'start': 1685951443.0566452, 'stop': 1685951443.059459, '$report_type': 'TestReport', 'item_index': 373, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_nested_loops_all', 'location': ('tests/test_loop.py', 236, 'test_nested_loops_all'), 'keywords': {'test_nested_loops_all': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/loop-inside-loop-all.cwl:45:13: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop-all.cwl:45:13: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop-all.cwl:56:7: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/i2' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _12] start\n\x1b[1;30mINFO\x1b[0m [workflow _12] starting step loop1_2\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] starting step loop2_4\n\x1b[1;30mINFO\x1b[0m [step loop2_4] start\n\x1b[1;30mINFO\x1b[0m [step loop2_4] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] starting step loop2_5\n\x1b[1;30mINFO\x1b[0m [step loop2_5] start\n\x1b[1;30mINFO\x1b[0m [step loop2_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_5] start\n\x1b[1;30mINFO\x1b[0m [step loop2_5] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] starting step loop2_6\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _12] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:45:13: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:45:13: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:56:7: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step loop1_2\nDEBUG cwltool:workflow_job.py:727 [step loop1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_4] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_4] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_4] starting step loop2_4\nDEBUG cwltool:workflow_job.py:727 [step loop2_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop2_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_4] Iteration 1 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_4] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 1\nDEBUG cwltool:workflow_job.py:925 [step loop2_4] inputs was {\n "i1": 2,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_4] outputs {\n "o1": [\n 2\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_5] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_5] inputs {\n "i1": 1,\n "i2": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_5] starting step loop2_5\nDEBUG cwltool:workflow_job.py:727 [step loop2_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 2\n}\nINFO cwltool:workflow_job.py:75 [step loop2_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_5] Iteration 2 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_5] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 2\nDEBUG cwltool:workflow_job.py:925 [step loop2_5] inputs was {\n "i1": 3,\n "i2": 2\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2,\n 3\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_5] outputs {\n "o1": [\n 2,\n 3\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2,\n 3\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_6] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_6] inputs {\n "i1": 1,\n "i2": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_6] starting step loop2_6\nDEBUG cwltool:workflow_job.py:727 [step loop2_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 3\n}\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_6] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop2_6] inputs was {\n "i1": 4,\n "i2": 3\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_6] outputs {\n "o1": [\n 2,\n 3,\n 4\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop1_2] loop condition $(inputs.i2 < 4) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop1_2] inputs was {\n "i1": 1,\n "i2": 4\n}\nDEBUG cwltool:workflow_job.py:564 [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n [\n 2\n ],\n [\n 2,\n 3\n ],\n [\n 2,\n 3,\n 4\n ]\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {\n "o1": [\n [\n 2\n ],\n [\n 2,\n 3\n ],\n [\n 2,\n 3,\n 4\n ]\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpns729pai\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwax8eltf\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp96zdj6k5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_ukam9wx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1771456070000568, 'start': 1685951442.150581, 'stop': 1685951443.327698, '$report_type': 'TestReport', 'item_index': 438, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_nested_loops_all', 'location': ('tests/test_loop.py', 236, 'test_nested_loops_all'), 'keywords': {'test_nested_loops_all': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/loop-inside-loop-all.cwl:45:13: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop-all.cwl:45:13: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1' previously defined\ntests/loop/loop-inside-loop-all.cwl:56:7: object id 'tests/loop/loop-inside-loop-all.cwl#loop1/i2' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _12] start\n\x1b[1;30mINFO\x1b[0m [workflow _12] starting step loop1_2\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] starting step loop2_4\n\x1b[1;30mINFO\x1b[0m [step loop2_4] start\n\x1b[1;30mINFO\x1b[0m [step loop2_4] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] starting step loop2_5\n\x1b[1;30mINFO\x1b[0m [step loop2_5] start\n\x1b[1;30mINFO\x1b[0m [step loop2_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_5] start\n\x1b[1;30mINFO\x1b[0m [step loop2_5] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] starting step loop2_6\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] start\n\x1b[1;30mINFO\x1b[0m [step loop2_6] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop2_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop1_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _12] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:45:13: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:45:13: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/loop-inside-loop-all.cwl:56:7: object id \'tests/loop/loop-inside-loop-all.cwl#loop1/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step loop1_2\nDEBUG cwltool:workflow_job.py:727 [step loop1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_4] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_4] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_4] starting step loop2_4\nDEBUG cwltool:workflow_job.py:727 [step loop2_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop2_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_4] Iteration 1 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_4] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 1\nDEBUG cwltool:workflow_job.py:925 [step loop2_4] inputs was {\n "i1": 2,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_4] outputs {\n "o1": [\n 2\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_5] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_5] inputs {\n "i1": 1,\n "i2": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_5] starting step loop2_5\nDEBUG cwltool:workflow_job.py:727 [step loop2_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 2\n}\nINFO cwltool:workflow_job.py:75 [step loop2_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_5] Iteration 2 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_5] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 2\nDEBUG cwltool:workflow_job.py:925 [step loop2_5] inputs was {\n "i1": 3,\n "i2": 2\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2,\n 3\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_5] outputs {\n "o1": [\n 2,\n 3\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2,\n 3\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop1_2] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop1_6] initialized from _:a302b80e-8c2b-4297-b5ec-1ffb252cca99\nINFO cwltool:workflow_job.py:765 [workflow loop1_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop1_6] inputs {\n "i1": 1,\n "i2": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop1_6] starting step loop2_6\nDEBUG cwltool:workflow_job.py:727 [step loop2_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step loop2_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/i2": 3\n}\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop2_6] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step loop2_6] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop2_6] loop condition $(inputs.i1 <= inputs.i2) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop2_6] inputs was {\n "i1": 4,\n "i2": 3\n}\nDEBUG cwltool:workflow_job.py:564 [step loop2_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/run/loop2/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop2_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop1_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop1_6] outputs {\n "o1": [\n 2,\n 3,\n 4\n ]\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n 2,\n 3,\n 4\n ]\n}\nINFO cwltool:workflow_job.py:1005 [step loop1_2] Iteration 3 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop1_2] loop condition $(inputs.i2 < 4) evaluated to False at iteration 3\nDEBUG cwltool:workflow_job.py:925 [step loop1_2] inputs was {\n "i1": 1,\n "i2": 4\n}\nDEBUG cwltool:workflow_job.py:564 [step loop1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/loop-inside-loop-all.cwl#loop1/o1": [\n [\n 2\n ],\n [\n 2,\n 3\n ],\n [\n 2,\n 3,\n 4\n ]\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {\n "o1": [\n [\n 2\n ],\n [\n 2,\n 3\n ],\n [\n 2,\n 3,\n 4\n ]\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpns729pai\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwax8eltf\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp96zdj6k5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_ukam9wx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00034923299972433597, 'start': 1685951443.328602, 'stop': 1685951443.328952, '$report_type': 'TestReport', 'item_index': 438, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_nested_loops_all - location: ('tests/test_loop.py', 236, 'test_nested_loops_all') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_multi_source_loop_input - location: ('tests/test_loop.py', 249, 'test_multi_source_loop_input') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input', 'location': ('tests/test_loop.py', 249, 'test_multi_source_loop_input'), 'keywords': {'test_multi_source_loop_input': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00032360799923480954, 'start': 1685951443.331817, 'stop': 1685951443.332142, '$report_type': 'TestReport', 'item_index': 439, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_newline_in_entry', 'location': ('tests/test_iwdr.py', 15, 'test_newline_in_entry'), 'keywords': {'test_newline_in_entry': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] {\n "message": "hello"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] initial work dir {\n "_:2a0436b5-e8e0-4317-9dff-723871e47051": [\n "CONFIGVAR=hello\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn/example.conf",\n "CreateFile",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mINFO\x1b[0m [job iwdr-entry.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn$ cat \\\n example.conf\nCONFIGVAR=hello\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mINFO\x1b[0m [job iwdr-entry.cwl] completed success\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] outputs {\n "out": "CONFIGVAR=hello\\n"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9_gw9k9h\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/bwdf_fga\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr-entry.cwl] initial work dir {\n "_:2a0436b5-e8e0-4317-9dff-723871e47051": [\n "CONFIGVAR=hello\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr-entry.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn$ cat \\\n example.conf\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr-entry.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr-entry.cwl] outputs {\n "out": "CONFIGVAR=hello\\n"\n}\nDEBUG cwltool:job.py:446 [job iwdr-entry.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9_gw9k9h\nDEBUG cwltool:job.py:454 [job iwdr-entry.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/bwdf_fga\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn')], 'duration': 0.8588610730002983, 'start': 1685951442.5531578, 'stop': 1685951443.411999, '$report_type': 'TestReport', 'item_index': 391, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_newline_in_entry', 'location': ('tests/test_iwdr.py', 15, 'test_newline_in_entry'), 'keywords': {'test_newline_in_entry': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:42]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] {\n "message": "hello"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] initial work dir {\n "_:2a0436b5-e8e0-4317-9dff-723871e47051": [\n "CONFIGVAR=hello\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn/example.conf",\n "CreateFile",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mINFO\x1b[0m [job iwdr-entry.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn$ cat \\\n example.conf\nCONFIGVAR=hello\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mINFO\x1b[0m [job iwdr-entry.cwl] completed success\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] outputs {\n "out": "CONFIGVAR=hello\\n"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9_gw9k9h\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job iwdr-entry.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/bwdf_fga\x1b[0m\n\x1b[32m[2023-06-05 09:50:43]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr-entry.cwl] initial work dir {\n "_:2a0436b5-e8e0-4317-9dff-723871e47051": [\n "CONFIGVAR=hello\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr-entry.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn$ cat \\\n example.conf\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr-entry.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr-entry.cwl] outputs {\n "out": "CONFIGVAR=hello\\n"\n}\nDEBUG cwltool:job.py:446 [job iwdr-entry.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9_gw9k9h\nDEBUG cwltool:job.py:454 [job iwdr-entry.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/bwdf_fga\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/oyc97oqn')], 'duration': 0.0004247679999025422, 'start': 1685951443.413008, 'stop': 1685951443.413434, '$report_type': 'TestReport', 'item_index': 391, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_iwdr.py::test_newline_in_entry - location: ('tests/test_iwdr.py', 15, 'test_newline_in_entry') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_iwdr.py::test_empty_file_creation - location: ('tests/test_iwdr.py', 22, 'test_empty_file_creation') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_empty_file_creation', 'location': ('tests/test_iwdr.py', 22, 'test_empty_file_creation'), 'keywords': {'test_empty_file_creation': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002311670004928601, 'start': 1685951443.4147048, 'stop': 1685951443.414937, '$report_type': 'TestReport', 'item_index': 392, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_tool', 'location': ('tests/test_mpi.py', 137, 'TestMpiRun.test_simple_mpi_tool'), 'keywords': {'test_simple_mpi_tool': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job mpi_simple.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_simple.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_simple.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_simple.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_simple.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_simple.cwl] /private/tmp/docker_tmpsrrf7xpl$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 2 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_simple.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_simple.cwl] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798",\n "basename": "412772b89f251957f4c82220883acbf443033798",\n "nameroot": "412772b89f251957f4c82220883acbf443033798",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$16cc94e5a27d65270f541b21404ad3b89fab0ddf",\n "size": 12,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_simple.cwl] Removing input staging directory /private/tmp/docker_tmpsl_eahho\nDEBUG cwltool:job.py:454 [job mpi_simple.cwl] Removing temporary directory /private/tmp/docker_tmphv_v29r_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_simple_mpi_tool0/412772b89f251957f4c82220883acbf443033798\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsrrf7xpl\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.2947465670004021, 'start': 1685951442.2788281, 'stop': 1685951443.573545, '$report_type': 'TestReport', 'item_index': 456, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_tool', 'location': ('tests/test_mpi.py', 137, 'TestMpiRun.test_simple_mpi_tool'), 'keywords': {'test_simple_mpi_tool': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job mpi_simple.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_simple.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_simple.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_simple.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_simple.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_simple.cwl] /private/tmp/docker_tmpsrrf7xpl$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 2 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_simple.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_simple.cwl] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798",\n "basename": "412772b89f251957f4c82220883acbf443033798",\n "nameroot": "412772b89f251957f4c82220883acbf443033798",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$16cc94e5a27d65270f541b21404ad3b89fab0ddf",\n "size": 12,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_simple.cwl] Removing input staging directory /private/tmp/docker_tmpsl_eahho\nDEBUG cwltool:job.py:454 [job mpi_simple.cwl] Removing temporary directory /private/tmp/docker_tmphv_v29r_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpsrrf7xpl/412772b89f251957f4c82220883acbf443033798 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_simple_mpi_tool0/412772b89f251957f4c82220883acbf443033798\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsrrf7xpl\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000572511999962444, 'start': 1685951443.5744262, 'stop': 1685951443.575, '$report_type': 'TestReport', 'item_index': 456, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::TestMpiRun::test_simple_mpi_tool - location: ('tests/test_mpi.py', 137, 'TestMpiRun.test_simple_mpi_tool') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::TestMpiRun::test_simple_mpi_nproc_expr - location: ('tests/test_mpi.py', 154, 'TestMpiRun.test_simple_mpi_nproc_expr') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_nproc_expr', 'location': ('tests/test_mpi.py', 154, 'TestMpiRun.test_simple_mpi_nproc_expr'), 'keywords': {'test_simple_mpi_nproc_expr': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016168849997484358, 'start': 1685951443.576514, 'stop': 1685951443.578132, '$report_type': 'TestReport', 'item_index': 457, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_error_graph_with_no_default', 'location': ('tests/test_misc_cli.py', 55, 'test_error_graph_with_no_default'), 'keywords': {'test_error_graph_with_no_default': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl'\nERROR cwltool:main.py:1211 Tool definition failed initialization:\nTool file contains graph of multiple objects, must specify one of #echo, #cat, #collision")], 'duration': 0.9360590020005475, 'start': 1685951442.8640919, 'stop': 1685951443.800129, '$report_type': 'TestReport', 'item_index': 451, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_error_graph_with_no_default', 'location': ('tests/test_misc_cli.py', 55, 'test_error_graph_with_no_default'), 'keywords': {'test_error_graph_with_no_default': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/packed_no_main.cwl'\nERROR cwltool:main.py:1211 Tool definition failed initialization:\nTool file contains graph of multiple objects, must specify one of #echo, #cat, #collision")], 'duration': 0.00019843600057356525, 'start': 1685951443.800568, 'stop': 1685951443.800767, '$report_type': 'TestReport', 'item_index': 451, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_misc_cli.py::test_error_graph_with_no_default - location: ('tests/test_misc_cli.py', 55, 'test_error_graph_with_no_default') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_misc_cli.py::test_skip_schemas_external_step - location: ('tests/test_misc_cli.py', 67, 'test_skip_schemas_external_step') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_skip_schemas_external_step', 'location': ('tests/test_misc_cli.py', 67, 'test_skip_schemas_external_step'), 'keywords': {'test_skip_schemas_external_step': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00022477499987871852, 'start': 1685951443.801759, 'stop': 1685951443.801984, '$report_type': 'TestReport', 'item_index': 452, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]'), 'keywords': {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_11\nDEBUG cwltool:workflow_job.py:727 [step task2_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_11\nDEBUG cwltool:command_line_tool.py:988 [job task2_9] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_9), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_11\nDEBUG cwltool:workflow_job.py:727 [step task1_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_11\nDEBUG cwltool:command_line_tool.py:988 [job task1_9] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_9] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_9), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task1_9] initial work dir {}\nINFO cwltool:job.py:266 [job task2_9] /private/tmp/docker_tmp6w_kuuwk$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp6w_kuuwk,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpimrbltf0,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-808365.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:266 [job task1_9] /private/tmp/docker_tmpqm8yecor$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqm8yecor,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpxft5vpeu,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-828561.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task2_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_9] completed success\nDEBUG cwltool:job.py:422 [job task2_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6w_kuuwk/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_11] completed success\nDEBUG cwltool:job.py:446 [job task2_9] Removing input staging directory /private/tmp/docker_tmpr2euvrmb\nDEBUG cwltool:job.py:454 [job task2_9] Removing temporary directory /private/tmp/docker_tmpimrbltf0\nINFO cwltool:job.py:905 [job task1_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_9] completed success\nDEBUG cwltool:job.py:422 [job task1_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqm8yecor/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_11] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_9] Removing input staging directory /private/tmp/docker_tmpfumwmmb0\nDEBUG cwltool:job.py:454 [job task1_9] Removing temporary directory /private/tmp/docker_tmpxft5vpeu\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqm8yecor\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp91c3ruq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6w_kuuwk\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.689709309999671, 'start': 1685951441.163031, 'stop': 1685951443.852674, '$report_type': 'TestReport', 'item_index': 277, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]'), 'keywords': {'test_cid_file_w_prefix[--parallel]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _11] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _11] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task2_11\nDEBUG cwltool:workflow_job.py:727 [step task2_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_11\nDEBUG cwltool:command_line_tool.py:988 [job task2_9] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _11] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_9), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _11] starting step task1_11\nDEBUG cwltool:workflow_job.py:727 [step task1_11] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_11] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_11] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_9] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_11\nDEBUG cwltool:command_line_tool.py:988 [job task1_9] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_9] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_9] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_9), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task1_9] initial work dir {}\nINFO cwltool:job.py:266 [job task2_9] /private/tmp/docker_tmp6w_kuuwk$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp6w_kuuwk,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpimrbltf0,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-808365.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:266 [job task1_9] /private/tmp/docker_tmpqm8yecor$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpqm8yecor,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpxft5vpeu,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral0/pytestcid-20230605095042-828561.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task2_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_9] completed success\nDEBUG cwltool:job.py:422 [job task2_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6w_kuuwk/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_11] completed success\nDEBUG cwltool:job.py:446 [job task2_9] Removing input staging directory /private/tmp/docker_tmpr2euvrmb\nDEBUG cwltool:job.py:454 [job task2_9] Removing temporary directory /private/tmp/docker_tmpimrbltf0\nINFO cwltool:job.py:905 [job task1_9] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_9] completed success\nDEBUG cwltool:job.py:422 [job task1_9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpqm8yecor/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_11] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_11] completed success\nINFO cwltool:workflow_job.py:539 [workflow _11] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _11] outputs {}\nDEBUG cwltool:job.py:446 [job task1_9] Removing input staging directory /private/tmp/docker_tmpfumwmmb0\nDEBUG cwltool:job.py:454 [job task1_9] Removing temporary directory /private/tmp/docker_tmpxft5vpeu\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqm8yecor\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp91c3ruq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6w_kuuwk\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007029949993011542, 'start': 1685951443.85393, 'stop': 1685951443.854634, '$report_type': 'TestReport', 'item_index': 277, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]'), 'keywords': {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0021138760002941126, 'start': 1685951443.8562508, 'stop': 1685951443.858367, '$report_type': 'TestReport', 'item_index': 278, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_expression_tool', 'location': ('tests/test_loop.py', 79, 'test_validate_loop_fail_on_expression_tool'), 'keywords': {'test_validate_loop_fail_on_expression_tool': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-expression-tool.cwl:11:7: object id 'tests/loop/invalid-loop-expression-tool.cwl#i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-expression-tool.cwl:16:1: checking field 'outputs'\ntests/loop/invalid-loop-expression-tool.cwl:17:3: checking object\n 'tests/loop/invalid-loop-expression-tool.cwl#o1'\ntests/loop/invalid-loop-expression-tool.cwl:19:5: Field 'outputSource' references unknown\n identifier 'subworkflow/o1', tried\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#o1/subworkflow/o1\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#subworkflow/o1\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-expression-tool.cwl:11:7: object id 'tests/loop/invalid-loop-expression-tool.cwl#i1' previously defined\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-expression-tool.cwl:16:1: checking field 'outputs'\ntests/loop/invalid-loop-expression-tool.cwl:17:3: checking object\n 'tests/loop/invalid-loop-expression-tool.cwl#o1'\ntests/loop/invalid-loop-expression-tool.cwl:19:5: Field 'outputSource' references unknown\n identifier 'subworkflow/o1', tried\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#o1/subworkflow/o1\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#subworkflow/o1")], 'duration': 0.9815994860000501, 'start': 1685951442.9462872, 'stop': 1685951443.9278631, '$report_type': 'TestReport', 'item_index': 425, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_expression_tool', 'location': ('tests/test_loop.py', 79, 'test_validate_loop_fail_on_expression_tool'), 'keywords': {'test_validate_loop_fail_on_expression_tool': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-expression-tool.cwl:11:7: object id 'tests/loop/invalid-loop-expression-tool.cwl#i1' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-expression-tool.cwl:16:1: checking field 'outputs'\ntests/loop/invalid-loop-expression-tool.cwl:17:3: checking object\n 'tests/loop/invalid-loop-expression-tool.cwl#o1'\ntests/loop/invalid-loop-expression-tool.cwl:19:5: Field 'outputSource' references unknown\n identifier 'subworkflow/o1', tried\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#o1/subworkflow/o1\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#subworkflow/o1\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-expression-tool.cwl:11:7: object id 'tests/loop/invalid-loop-expression-tool.cwl#i1' previously defined\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-expression-tool.cwl:16:1: checking field 'outputs'\ntests/loop/invalid-loop-expression-tool.cwl:17:3: checking object\n 'tests/loop/invalid-loop-expression-tool.cwl#o1'\ntests/loop/invalid-loop-expression-tool.cwl:19:5: Field 'outputSource' references unknown\n identifier 'subworkflow/o1', tried\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#o1/subworkflow/o1\n file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-expression-tool.cwl#subworkflow/o1")], 'duration': 0.00020623100044758758, 'start': 1685951443.928481, 'stop': 1685951443.928688, '$report_type': 'TestReport', 'item_index': 425, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_hint', 'location': ('tests/test_loop.py', 89, 'test_validate_loop_fail_on_hint'), 'keywords': {'test_validate_loop_fail_on_hint': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00033236099989153445, 'start': 1685951443.9295738, 'stop': 1685951443.929908, '$report_type': 'TestReport', 'item_index': 426, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_validate_loop_fail_on_expression_tool - location: ('tests/test_loop.py', 79, 'test_validate_loop_fail_on_expression_tool') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_validate_loop_fail_on_hint - location: ('tests/test_loop.py', 89, 'test_validate_loop_fail_on_hint') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_dir_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 186, 'test_disable_dir_creation_in_outdir_with_ext'), 'keywords': {'test_disable_dir_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp",\n "basename": "inp",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp/blurb",\n "basename": "blurb",\n "path": "/private/tmp/docker_tmp9wjf3kni/inp/blurb"\n }\n ],\n "path": "/private/tmp/docker_tmp9wjf3kni/inp"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl'\n\x1b[1;30mINFO\x1b[0m [job updatedir_inplace.cwl] /private/tmp/docker_tmp9wjf3kni$ touch \\\n inp/blurb\n\x1b[1;30mINFO\x1b[0m [job updatedir_inplace.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl",\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updatedir_inplace.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updatedir_inplace.cwl] {\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "basename": "tmp",\n "listing": []\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updatedir_inplace.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "/private/tmp/docker_tmp9wjf3kni/inp",\n "WritableDirectory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updatedir_inplace.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp/blurb"\n }\n]\nDEBUG cwltool:job.py:215 [job updatedir_inplace.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "/private/tmp/docker_tmp9wjf3kni/inp",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updatedir_inplace.cwl] /private/tmp/docker_tmp9wjf3kni$ touch \\\n inp/blurb\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job updatedir_inplace.cwl] completed success\nDEBUG cwltool:job.py:422 [job updatedir_inplace.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp",\n "basename": "inp",\n "nameroot": "inp",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job updatedir_inplace.cwl] Removing input staging directory /private/tmp/docker_tmpg_pphm3n\nDEBUG cwltool:job.py:454 [job updatedir_inplace.cwl] Removing temporary directory /private/tmp/docker_tmps3ugovj7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9wjf3kni\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9035728740000195, 'start': 1685951443.060123, 'stop': 1685951443.963676, '$report_type': 'TestReport', 'item_index': 373, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_disable_dir_creation_in_outdir_with_ext', 'location': ('tests/test_ext.py', 186, 'test_disable_dir_creation_in_outdir_with_ext'), 'keywords': {'test_disable_dir_creation_in_outdir_with_ext': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp",\n "basename": "inp",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp/blurb",\n "basename": "blurb",\n "path": "/private/tmp/docker_tmp9wjf3kni/inp/blurb"\n }\n ],\n "path": "/private/tmp/docker_tmp9wjf3kni/inp"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl'\n\x1b[1;30mINFO\x1b[0m [job updatedir_inplace.cwl] /private/tmp/docker_tmp9wjf3kni$ touch \\\n inp/blurb\n\x1b[1;30mINFO\x1b[0m [job updatedir_inplace.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl",\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job updatedir_inplace.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updatedir_inplace.cwl\nDEBUG cwltool:command_line_tool.py:988 [job updatedir_inplace.cwl] {\n "r": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "basename": "tmp",\n "listing": []\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job updatedir_inplace.cwl] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "/private/tmp/docker_tmp9wjf3kni/inp",\n "WritableDirectory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job updatedir_inplace.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp/blurb"\n }\n]\nDEBUG cwltool:job.py:215 [job updatedir_inplace.cwl] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_disable_dir_creation_in_o0/tmp",\n "/private/tmp/docker_tmp9wjf3kni/inp",\n "WritableDirectory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job updatedir_inplace.cwl] /private/tmp/docker_tmp9wjf3kni$ touch \\\n inp/blurb\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job updatedir_inplace.cwl] completed success\nDEBUG cwltool:job.py:422 [job updatedir_inplace.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp9wjf3kni/inp",\n "basename": "inp",\n "nameroot": "inp",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job updatedir_inplace.cwl] Removing input staging directory /private/tmp/docker_tmpg_pphm3n\nDEBUG cwltool:job.py:454 [job updatedir_inplace.cwl] Removing temporary directory /private/tmp/docker_tmps3ugovj7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9wjf3kni\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0004848630005653831, 'start': 1685951443.964662, 'stop': 1685951443.965148, '$report_type': 'TestReport', 'item_index': 373, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_disable_dir_creation_in_outdir_with_ext - location: ('tests/test_ext.py', 186, 'test_disable_dir_creation_in_outdir_with_ext') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_ext.py::test_write_write_conflict - location: ('tests/test_ext.py', 207, 'test_write_write_conflict') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_write_write_conflict', 'location': ('tests/test_ext.py', 207, 'test_write_write_conflict'), 'keywords': {'test_write_write_conflict': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012940050000906922, 'start': 1685951443.9662888, 'stop': 1685951443.967584, '$report_type': 'TestReport', 'item_index': 374, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_empty_file_creation', 'location': ('tests/test_iwdr.py', 22, 'test_empty_file_creation'), 'keywords': {'test_empty_file_creation': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-empty.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-empty.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-empty.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-empty.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "empty_file"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr-empty.cwl] initial work dir {\n "_:4fafb878-bba4-4c1b-8b10-31e9ea2e72c1": [\n "",\n "/private/tmp/docker_tmpdtxp2fa3/empty_file",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr-empty.cwl] /private/tmp/docker_tmpdtxp2fa3$ cat \\\n empty_file\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr-empty.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr-empty.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr-empty.cwl] Removing input staging directory /private/tmp/docker_tmpnky3nerk\nDEBUG cwltool:job.py:454 [job iwdr-empty.cwl] Removing temporary directory /private/tmp/docker_tmpwhfbqro0\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdtxp2fa3\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7176641799997014, 'start': 1685951443.415307, 'stop': 1685951444.1329558, '$report_type': 'TestReport', 'item_index': 392, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_empty_file_creation', 'location': ('tests/test_iwdr.py', 22, 'test_empty_file_creation'), 'keywords': {'test_empty_file_creation': 1, 'skipif': 1, 'pytestmark': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-empty.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-empty.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-empty.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-empty.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-empty.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "empty_file"\n }\n]\nDEBUG cwltool:job.py:215 [job iwdr-empty.cwl] initial work dir {\n "_:4fafb878-bba4-4c1b-8b10-31e9ea2e72c1": [\n "",\n "/private/tmp/docker_tmpdtxp2fa3/empty_file",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job iwdr-empty.cwl] /private/tmp/docker_tmpdtxp2fa3$ cat \\\n empty_file\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job iwdr-empty.cwl] completed success\nDEBUG cwltool:job.py:422 [job iwdr-empty.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job iwdr-empty.cwl] Removing input staging directory /private/tmp/docker_tmpnky3nerk\nDEBUG cwltool:job.py:454 [job iwdr-empty.cwl] Removing temporary directory /private/tmp/docker_tmpwhfbqro0\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdtxp2fa3\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0004950769998686155, 'start': 1685951444.133989, 'stop': 1685951444.134485, '$report_type': 'TestReport', 'item_index': 392, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_iwdr.py::test_empty_file_creation - location: ('tests/test_iwdr.py', 22, 'test_empty_file_creation') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_iwdr.py::test_passthrough_successive - location: ('tests/test_iwdr.py', 29, 'test_passthrough_successive') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_passthrough_successive', 'location': ('tests/test_iwdr.py', 29, 'test_passthrough_successive'), 'keywords': {'test_passthrough_successive': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018658310000319034, 'start': 1685951444.136501, 'stop': 1685951444.138368, '$report_type': 'TestReport', 'item_index': 393, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input', 'location': ('tests/test_loop.py', 249, 'test_multi_source_loop_input'), 'keywords': {'test_multi_source_loop_input': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/multi-source-loop.cwl:60:7: object id \'tests/loop/multi-source-loop.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/multi-source-loop.cwl:61:11: Source \'osmall\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\ntests/loop/multi-source-loop.cwl:61:19: Source \'obig\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _13] start\n\x1b[1;30mINFO\x1b[0m [workflow _13] starting step loop\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step small_values\n\x1b[1;30mINFO\x1b[0m [step small_values] start\n\x1b[1;30mINFO\x1b[0m [step small_values] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step big_values\n\x1b[1;30mINFO\x1b[0m [step big_values] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step small_values_2\n\x1b[1;30mINFO\x1b[0m [step small_values_2] start\n\x1b[1;30mINFO\x1b[0m [step small_values_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step big_values_2\n\x1b[1;30mINFO\x1b[0m [step big_values_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step small_values_3\n\x1b[1;30mINFO\x1b[0m [step small_values_3] start\n\x1b[1;30mINFO\x1b[0m [step small_values_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step big_values_3\n\x1b[1;30mINFO\x1b[0m [step big_values_3] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_3] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step small_values_4\n\x1b[1;30mINFO\x1b[0m [step small_values_4] start\n\x1b[1;30mINFO\x1b[0m [step small_values_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step big_values_4\n\x1b[1;30mINFO\x1b[0m [step big_values_4] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_4] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step small_values_5\n\x1b[1;30mINFO\x1b[0m [step small_values_5] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_5] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step big_values_5\n\x1b[1;30mINFO\x1b[0m [step big_values_5] start\n\x1b[1;30mINFO\x1b[0m [step big_values_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step small_values_6\n\x1b[1;30mINFO\x1b[0m [step small_values_6] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_6] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step big_values_6\n\x1b[1;30mINFO\x1b[0m [step big_values_6] start\n\x1b[1;30mINFO\x1b[0m [step big_values_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step small_values_7\n\x1b[1;30mINFO\x1b[0m [step small_values_7] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_7] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step big_values_7\n\x1b[1;30mINFO\x1b[0m [step big_values_7] start\n\x1b[1;30mINFO\x1b[0m [step big_values_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] starting step small_values_8\n\x1b[1;30mINFO\x1b[0m [step small_values_8] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_8] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] starting step big_values_8\n\x1b[1;30mINFO\x1b[0m [step big_values_8] start\n\x1b[1;30mINFO\x1b[0m [step big_values_8] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] starting step small_values_9\n\x1b[1;30mINFO\x1b[0m [step small_values_9] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_9] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] starting step big_values_9\n\x1b[1;30mINFO\x1b[0m [step big_values_9] start\n\x1b[1;30mINFO\x1b[0m [step big_values_9] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _13] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/multi-source-loop.cwl:60:7: object id \'tests/loop/multi-source-loop.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/multi-source-loop.cwl:61:11: Source \'osmall\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\ntests/loop/multi-source-loop.cwl:61:19: Source \'obig\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step loop\nDEBUG cwltool:workflow_job.py:727 [step loop] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step small_values\nDEBUG cwltool:workflow_job.py:727 [step small_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step small_values] start\nDEBUG cwltool:workflow_job.py:564 [step small_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step small_values] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step big_values\nDEBUG cwltool:workflow_job.py:727 [step big_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop] outputs {\n "obig": null,\n "osmall": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_2] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_2] inputs {\n "i1": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step small_values_2\nDEBUG cwltool:workflow_job.py:727 [step small_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 2\n}\nINFO cwltool:workflow_job.py:75 [step small_values_2] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 3\n}\nINFO cwltool:workflow_job.py:572 [step small_values_2] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step big_values_2\nDEBUG cwltool:workflow_job.py:727 [step big_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 2\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_2] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_2] inputs was {\n "i1": 2\n}\nINFO cwltool:workflow_job.py:744 [step big_values_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_2] outputs {\n "obig": null,\n "osmall": 3\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_3] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_3] inputs {\n "i1": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step small_values_3\nDEBUG cwltool:workflow_job.py:727 [step small_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 3\n}\nINFO cwltool:workflow_job.py:75 [step small_values_3] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 4\n}\nINFO cwltool:workflow_job.py:572 [step small_values_3] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step big_values_3\nDEBUG cwltool:workflow_job.py:727 [step big_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 3\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_3] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_3] inputs was {\n "i1": 3\n}\nINFO cwltool:workflow_job.py:744 [step big_values_3] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_3] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_3] outputs {\n "obig": null,\n "osmall": 4\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_4] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_4] inputs {\n "i1": 4\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step small_values_4\nDEBUG cwltool:workflow_job.py:727 [step small_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 4\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 4\n}\nINFO cwltool:workflow_job.py:75 [step small_values_4] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 5\n}\nINFO cwltool:workflow_job.py:572 [step small_values_4] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step big_values_4\nDEBUG cwltool:workflow_job.py:727 [step big_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 4\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_4] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_4] inputs was {\n "i1": 4\n}\nINFO cwltool:workflow_job.py:744 [step big_values_4] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_4] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_4] outputs {\n "obig": null,\n "osmall": 5\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_5] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_5] inputs {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step small_values_5\nDEBUG cwltool:workflow_job.py:727 [step small_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_5] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_5] inputs was {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:744 [step small_values_5] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_5] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step big_values_5\nDEBUG cwltool:workflow_job.py:727 [step big_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 5\n}\nINFO cwltool:workflow_job.py:75 [step big_values_5] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 8\n}\nINFO cwltool:workflow_job.py:572 [step big_values_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_5] outputs {\n "obig": 8,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 8\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_6] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_6] inputs {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step small_values_6\nDEBUG cwltool:workflow_job.py:727 [step small_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_6] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_6] inputs was {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:744 [step small_values_6] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_6] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step big_values_6\nDEBUG cwltool:workflow_job.py:727 [step big_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 8\n}\nINFO cwltool:workflow_job.py:75 [step big_values_6] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 11\n}\nINFO cwltool:workflow_job.py:572 [step big_values_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_6] outputs {\n "obig": 11,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 11\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_7] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_7] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_7] inputs {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step small_values_7\nDEBUG cwltool:workflow_job.py:727 [step small_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_7] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_7] inputs was {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:744 [step small_values_7] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_7] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step big_values_7\nDEBUG cwltool:workflow_job.py:727 [step big_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 11\n}\nINFO cwltool:workflow_job.py:75 [step big_values_7] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 14\n}\nINFO cwltool:workflow_job.py:572 [step big_values_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_7] outputs {\n "obig": 14,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 14\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_8] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_8] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_8] inputs {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_8] starting step small_values_8\nDEBUG cwltool:workflow_job.py:727 [step small_values_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_8] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_8] inputs was {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:744 [step small_values_8] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_8] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_8] starting step big_values_8\nDEBUG cwltool:workflow_job.py:727 [step big_values_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_8] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 14\n}\nINFO cwltool:workflow_job.py:75 [step big_values_8] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 17\n}\nINFO cwltool:workflow_job.py:572 [step big_values_8] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_8] outputs {\n "obig": 17,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 17\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_9] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_9] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_9] inputs {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_9] starting step small_values_9\nDEBUG cwltool:workflow_job.py:727 [step small_values_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_9] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_9] inputs was {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:744 [step small_values_9] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_9] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_9] starting step big_values_9\nDEBUG cwltool:workflow_job.py:727 [step big_values_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 17\n}\nINFO cwltool:workflow_job.py:75 [step big_values_9] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 20\n}\nINFO cwltool:workflow_job.py:572 [step big_values_9] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_9] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_9] outputs {\n "obig": 20,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 20\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop] loop condition $(inputs.i1 < 20) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step loop] inputs was {\n "i1": 20\n}\nDEBUG cwltool:workflow_job.py:564 [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": [\n 2,\n 3,\n 4,\n 5,\n null,\n null,\n null,\n null,\n null\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": [\n null,\n null,\n null,\n null,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {\n "o1": [\n 2,\n 3,\n 4,\n 5,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsrpsturk\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp26tpehja\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpg55oc7b_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbhqm8htr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnnke968d\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpujampaqh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3w_tube1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwdhb0cy6\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsom8y9_3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm4vwtqib\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1180563010002516, 'start': 1685951443.332685, 'stop': 1685951444.450714, '$report_type': 'TestReport', 'item_index': 439, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_multi_source_loop_input', 'location': ('tests/test_loop.py', 249, 'test_multi_source_loop_input'), 'keywords': {'test_multi_source_loop_input': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/multi-source-loop.cwl:60:7: object id \'tests/loop/multi-source-loop.cwl#loop/i1\' previously defined\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/loop/multi-source-loop.cwl:61:11: Source \'osmall\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\ntests/loop/multi-source-loop.cwl:61:19: Source \'obig\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _13] start\n\x1b[1;30mINFO\x1b[0m [workflow _13] starting step loop\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step small_values\n\x1b[1;30mINFO\x1b[0m [step small_values] start\n\x1b[1;30mINFO\x1b[0m [step small_values] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop] starting step big_values\n\x1b[1;30mINFO\x1b[0m [step big_values] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step small_values_2\n\x1b[1;30mINFO\x1b[0m [step small_values_2] start\n\x1b[1;30mINFO\x1b[0m [step small_values_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] starting step big_values_2\n\x1b[1;30mINFO\x1b[0m [step big_values_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_2] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step small_values_3\n\x1b[1;30mINFO\x1b[0m [step small_values_3] start\n\x1b[1;30mINFO\x1b[0m [step small_values_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] starting step big_values_3\n\x1b[1;30mINFO\x1b[0m [step big_values_3] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_3] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_3] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step small_values_4\n\x1b[1;30mINFO\x1b[0m [step small_values_4] start\n\x1b[1;30mINFO\x1b[0m [step small_values_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] starting step big_values_4\n\x1b[1;30mINFO\x1b[0m [step big_values_4] will be skipped\n\x1b[1;30mINFO\x1b[0m [step big_values_4] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_4] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step small_values_5\n\x1b[1;30mINFO\x1b[0m [step small_values_5] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_5] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] starting step big_values_5\n\x1b[1;30mINFO\x1b[0m [step big_values_5] start\n\x1b[1;30mINFO\x1b[0m [step big_values_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_5] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step small_values_6\n\x1b[1;30mINFO\x1b[0m [step small_values_6] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_6] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] starting step big_values_6\n\x1b[1;30mINFO\x1b[0m [step big_values_6] start\n\x1b[1;30mINFO\x1b[0m [step big_values_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_6] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step small_values_7\n\x1b[1;30mINFO\x1b[0m [step small_values_7] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_7] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] starting step big_values_7\n\x1b[1;30mINFO\x1b[0m [step big_values_7] start\n\x1b[1;30mINFO\x1b[0m [step big_values_7] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_7] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] starting step small_values_8\n\x1b[1;30mINFO\x1b[0m [step small_values_8] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_8] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] starting step big_values_8\n\x1b[1;30mINFO\x1b[0m [step big_values_8] start\n\x1b[1;30mINFO\x1b[0m [step big_values_8] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_8] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] start\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] starting step small_values_9\n\x1b[1;30mINFO\x1b[0m [step small_values_9] will be skipped\n\x1b[1;30mINFO\x1b[0m [step small_values_9] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] starting step big_values_9\n\x1b[1;30mINFO\x1b[0m [step big_values_9] start\n\x1b[1;30mINFO\x1b[0m [step big_values_9] completed success\n\x1b[1;30mINFO\x1b[0m [workflow loop_9] completed success\n\x1b[1;30mINFO\x1b[0m [step loop] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step loop] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _13] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/multi-source-loop.cwl:60:7: object id \'tests/loop/multi-source-loop.cwl#loop/i1\' previously defined\nWARNING cwltool:checker.py:319 Workflow checker warning:\ntests/loop/multi-source-loop.cwl:61:11: Source \'osmall\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\ntests/loop/multi-source-loop.cwl:61:19: Source \'obig\' of type {"type": "array", "items": ["null",\n "int"]} may be incompatible\ntests/loop/multi-source-loop.cwl:15:5: with sink \'o1\' of type {"type": "array", "items": "int"}\n source has linkMerge method merge_flattened\n pickValue is: all_non_null\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step loop\nDEBUG cwltool:workflow_job.py:727 [step loop] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step loop] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step small_values\nDEBUG cwltool:workflow_job.py:727 [step small_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step small_values] start\nDEBUG cwltool:workflow_job.py:564 [step small_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 2\n}\nINFO cwltool:workflow_job.py:572 [step small_values] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop] starting step big_values\nDEBUG cwltool:workflow_job.py:727 [step big_values] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 1\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values] inputs was {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:744 [step big_values] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop] outputs {\n "obig": null,\n "osmall": 2\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_2] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_2] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_2] inputs {\n "i1": 2\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step small_values_2\nDEBUG cwltool:workflow_job.py:727 [step small_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 2\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 2\n}\nINFO cwltool:workflow_job.py:75 [step small_values_2] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 3\n}\nINFO cwltool:workflow_job.py:572 [step small_values_2] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_2] starting step big_values_2\nDEBUG cwltool:workflow_job.py:727 [step big_values_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 2\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_2] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_2] inputs was {\n "i1": 2\n}\nINFO cwltool:workflow_job.py:744 [step big_values_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_2] outputs {\n "obig": null,\n "osmall": 3\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_3] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_3] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_3] inputs {\n "i1": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step small_values_3\nDEBUG cwltool:workflow_job.py:727 [step small_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 3\n}\nINFO cwltool:workflow_job.py:75 [step small_values_3] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 4\n}\nINFO cwltool:workflow_job.py:572 [step small_values_3] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_3] starting step big_values_3\nDEBUG cwltool:workflow_job.py:727 [step big_values_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 3\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_3] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_3] inputs was {\n "i1": 3\n}\nINFO cwltool:workflow_job.py:744 [step big_values_3] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_3] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_3] outputs {\n "obig": null,\n "osmall": 4\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_4] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_4] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_4] inputs {\n "i1": 4\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step small_values_4\nDEBUG cwltool:workflow_job.py:727 [step small_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 4\n}\nDEBUG cwltool:workflow_job.py:732 [step small_values_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 4\n}\nINFO cwltool:workflow_job.py:75 [step small_values_4] start\nDEBUG cwltool:workflow_job.py:564 [step small_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": 5\n}\nINFO cwltool:workflow_job.py:572 [step small_values_4] completed success\nINFO cwltool:workflow_job.py:613 [workflow loop_4] starting step big_values_4\nDEBUG cwltool:workflow_job.py:727 [step big_values_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 4\n}\nDEBUG cwltool:workflow_job.py:678 [step big_values_4] conditional $(inputs.i1 >= 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step big_values_4] inputs was {\n "i1": 4\n}\nINFO cwltool:workflow_job.py:744 [step big_values_4] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step big_values_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step big_values_4] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow loop_4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_4] outputs {\n "obig": null,\n "osmall": 5\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": null\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_5] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_5] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_5] inputs {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step small_values_5\nDEBUG cwltool:workflow_job.py:727 [step small_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_5] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_5] inputs was {\n "i1": 5\n}\nINFO cwltool:workflow_job.py:744 [step small_values_5] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_5] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_5] starting step big_values_5\nDEBUG cwltool:workflow_job.py:727 [step big_values_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 5\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 5\n}\nINFO cwltool:workflow_job.py:75 [step big_values_5] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 8\n}\nINFO cwltool:workflow_job.py:572 [step big_values_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_5] outputs {\n "obig": 8,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 8\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_6] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_6] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_6] inputs {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step small_values_6\nDEBUG cwltool:workflow_job.py:727 [step small_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_6] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_6] inputs was {\n "i1": 8\n}\nINFO cwltool:workflow_job.py:744 [step small_values_6] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_6] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_6] starting step big_values_6\nDEBUG cwltool:workflow_job.py:727 [step big_values_6] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 8\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_6] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 8\n}\nINFO cwltool:workflow_job.py:75 [step big_values_6] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 11\n}\nINFO cwltool:workflow_job.py:572 [step big_values_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_6] outputs {\n "obig": 11,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 11\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_7] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_7] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_7] inputs {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step small_values_7\nDEBUG cwltool:workflow_job.py:727 [step small_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_7] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_7] inputs was {\n "i1": 11\n}\nINFO cwltool:workflow_job.py:744 [step small_values_7] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_7] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_7] starting step big_values_7\nDEBUG cwltool:workflow_job.py:727 [step big_values_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 11\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 11\n}\nINFO cwltool:workflow_job.py:75 [step big_values_7] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 14\n}\nINFO cwltool:workflow_job.py:572 [step big_values_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_7] outputs {\n "obig": 14,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 14\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_8] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_8] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_8] inputs {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_8] starting step small_values_8\nDEBUG cwltool:workflow_job.py:727 [step small_values_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_8] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_8] inputs was {\n "i1": 14\n}\nINFO cwltool:workflow_job.py:744 [step small_values_8] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_8] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_8] starting step big_values_8\nDEBUG cwltool:workflow_job.py:727 [step big_values_8] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 14\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_8] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 14\n}\nINFO cwltool:workflow_job.py:75 [step big_values_8] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_8] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 17\n}\nINFO cwltool:workflow_job.py:572 [step big_values_8] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_8] outputs {\n "obig": 17,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 17\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step loop] start\nDEBUG cwltool:workflow_job.py:498 [workflow loop_9] initialized from _:2e080c82-b9b3-40e1-b2f6-05fa9062c9c1\nINFO cwltool:workflow_job.py:765 [workflow loop_9] start\nDEBUG cwltool:workflow_job.py:777 [workflow loop_9] inputs {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:613 [workflow loop_9] starting step small_values_9\nDEBUG cwltool:workflow_job.py:727 [step small_values_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:678 [step small_values_9] conditional $(inputs.i1 < 5) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step small_values_9] inputs was {\n "i1": 17\n}\nINFO cwltool:workflow_job.py:744 [step small_values_9] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step small_values_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/small_values/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step small_values_9] completed skipped\nINFO cwltool:workflow_job.py:613 [workflow loop_9] starting step big_values_9\nDEBUG cwltool:workflow_job.py:727 [step big_values_9] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 17\n}\nDEBUG cwltool:workflow_job.py:732 [step big_values_9] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/i1": 17\n}\nINFO cwltool:workflow_job.py:75 [step big_values_9] start\nDEBUG cwltool:workflow_job.py:564 [step big_values_9] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/run/big_values/o1": 20\n}\nINFO cwltool:workflow_job.py:572 [step big_values_9] completed success\nINFO cwltool:workflow_job.py:539 [workflow loop_9] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow loop_9] outputs {\n "obig": 20,\n "osmall": null\n}\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": null,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": 20\n}\nINFO cwltool:workflow_job.py:1005 [step loop] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step loop] loop condition $(inputs.i1 < 20) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step loop] inputs was {\n "i1": 20\n}\nDEBUG cwltool:workflow_job.py:564 [step loop] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/osmall": [\n 2,\n 3,\n 4,\n 5,\n null,\n null,\n null,\n null,\n null\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/multi-source-loop.cwl#loop/obig": [\n null,\n null,\n null,\n null,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nINFO cwltool:workflow_job.py:572 [step loop] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {\n "o1": [\n 2,\n 3,\n 4,\n 5,\n 8,\n 11,\n 14,\n 17,\n 20\n ]\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsrpsturk\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp26tpehja\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpg55oc7b_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbhqm8htr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnnke968d\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpujampaqh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3w_tube1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwdhb0cy6\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsom8y9_3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm4vwtqib\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000421602999267634, 'start': 1685951444.452204, 'stop': 1685951444.452627, '$report_type': 'TestReport', 'item_index': 439, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_multi_source_loop_input - location: ('tests/test_loop.py', 249, 'test_multi_source_loop_input') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters1-result1]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters1-result1]'), 'keywords': {'test_overrides[parameters1-result1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters1-result1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006827130000601755, 'start': 1685951444.4550772, 'stop': 1685951444.455761, '$report_type': 'TestReport', 'item_index': 468, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides[parameters1-result1] - location: ('tests/test_override.py', 76, 'test_overrides[parameters1-result1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_nproc_expr', 'location': ('tests/test_mpi.py', 154, 'TestMpiRun.test_simple_mpi_nproc_expr'), 'keywords': {'test_simple_mpi_nproc_expr': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job mpi_expr.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_expr.cwl] {\n "processes": 4\n}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_expr.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_expr.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_expr.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_expr.cwl] /private/tmp/docker_tmpaigw30gn$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 4 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_expr.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_expr.cwl] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$05b0c06f1a5d09cb506e00062429a2281b169cb6",\n "size": 24,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_expr.cwl] Removing input staging directory /private/tmp/docker_tmpuhnsmj7a\nDEBUG cwltool:job.py:454 [job mpi_expr.cwl] Removing temporary directory /private/tmp/docker_tmpubimcz5_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_simple_mpi_nproc_expr0/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaigw30gn\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1397649960008494, 'start': 1685951443.578856, 'stop': 1685951444.718595, '$report_type': 'TestReport', 'item_index': 457, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_simple_mpi_nproc_expr', 'location': ('tests/test_mpi.py', 154, 'TestMpiRun.test_simple_mpi_nproc_expr'), 'keywords': {'test_simple_mpi_nproc_expr': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job mpi_expr.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_expr.cwl] {\n "processes": 4\n}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_expr.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_expr.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_expr.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_expr.cwl] /private/tmp/docker_tmpaigw30gn$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 4 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_expr.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_expr.cwl] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$05b0c06f1a5d09cb506e00062429a2281b169cb6",\n "size": 24,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_expr.cwl] Removing input staging directory /private/tmp/docker_tmpuhnsmj7a\nDEBUG cwltool:job.py:454 [job mpi_expr.cwl] Removing temporary directory /private/tmp/docker_tmpubimcz5_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_simple_mpi_nproc_expr0/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaigw30gn\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005845309997312143, 'start': 1685951444.719844, 'stop': 1685951444.7204301, '$report_type': 'TestReport', 'item_index': 457, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::TestMpiRun::test_simple_mpi_nproc_expr - location: ('tests/test_mpi.py', 154, 'TestMpiRun.test_simple_mpi_nproc_expr') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::TestMpiRun::test_mpi_workflow - location: ('tests/test_mpi.py', 174, 'TestMpiRun.test_mpi_workflow') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_mpi_workflow', 'location': ('tests/test_mpi.py', 174, 'TestMpiRun.test_mpi_workflow'), 'keywords': {'test_mpi_workflow': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0020967160007785424, 'start': 1685951444.7220821, 'stop': 1685951444.7241821, '$report_type': 'TestReport', 'item_index': 458, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_skip_schemas_external_step', 'location': ('tests/test_misc_cli.py', 67, 'test_skip_schemas_external_step'), 'keywords': {'test_skip_schemas_external_step': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "Warning: Field '$schemas' contains undefined reference to 'https://bad.example.com/missing.ttl'\nWarning: Field '$schemas' contains undefined reference to 'https://schema.org/docs/'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_step_bad_schema.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_step_bad_schema.cwl'\nWARNING salad:ref_resolver.py:1114 Warning: Field '$schemas' contains undefined reference to 'https://bad.example.com/missing.ttl'\nWarning: Field '$schemas' contains undefined reference to 'https://schema.org/docs/'")], 'duration': 0.9561014020000584, 'start': 1685951443.8023129, 'stop': 1685951444.758394, '$report_type': 'TestReport', 'item_index': 452, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_misc_cli.py::test_skip_schemas_external_step', 'location': ('tests/test_misc_cli.py', 67, 'test_skip_schemas_external_step'), 'keywords': {'test_skip_schemas_external_step': 1, 'test_misc_cli.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "Warning: Field '$schemas' contains undefined reference to 'https://bad.example.com/missing.ttl'\nWarning: Field '$schemas' contains undefined reference to 'https://schema.org/docs/'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_step_bad_schema.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_step_bad_schema.cwl'\nWARNING salad:ref_resolver.py:1114 Warning: Field '$schemas' contains undefined reference to 'https://bad.example.com/missing.ttl'\nWarning: Field '$schemas' contains undefined reference to 'https://schema.org/docs/'")], 'duration': 0.0003151399996568216, 'start': 1685951444.758986, 'stop': 1685951444.7593029, '$report_type': 'TestReport', 'item_index': 452, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_misc_cli.py::test_skip_schemas_external_step - location: ('tests/test_misc_cli.py', 67, 'test_skip_schemas_external_step') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::test_mpi_conf_defaults - location: ('tests/test_mpi.py', 25, 'test_mpi_conf_defaults') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_defaults', 'location': ('tests/test_mpi.py', 25, 'test_mpi_conf_defaults'), 'keywords': {'test_mpi_conf_defaults': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00028388800001266645, 'start': 1685951444.7607198, 'stop': 1685951444.7610052, '$report_type': 'TestReport', 'item_index': 453, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_defaults', 'location': ('tests/test_mpi.py', 25, 'test_mpi_conf_defaults'), 'keywords': {'test_mpi_conf_defaults': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00022293799975159345, 'start': 1685951444.7613308, 'stop': 1685951444.761555, '$report_type': 'TestReport', 'item_index': 453, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_defaults', 'location': ('tests/test_mpi.py', 25, 'test_mpi_conf_defaults'), 'keywords': {'test_mpi_conf_defaults': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0001631519999136799, 'start': 1685951444.761871, 'stop': 1685951444.762035, '$report_type': 'TestReport', 'item_index': 453, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::test_mpi_conf_defaults - location: ('tests/test_mpi.py', 25, 'test_mpi_conf_defaults') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::test_mpi_conf_unknownkeys - location: ('tests/test_mpi.py', 36, 'test_mpi_conf_unknownkeys') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_unknownkeys', 'location': ('tests/test_mpi.py', 36, 'test_mpi_conf_unknownkeys'), 'keywords': {'test_mpi_conf_unknownkeys': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00022150800032250118, 'start': 1685951444.762811, 'stop': 1685951444.763034, '$report_type': 'TestReport', 'item_index': 454, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_unknownkeys', 'location': ('tests/test_mpi.py', 36, 'test_mpi_conf_unknownkeys'), 'keywords': {'test_mpi_conf_unknownkeys': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006723149999743327, 'start': 1685951444.763655, 'stop': 1685951444.764328, '$report_type': 'TestReport', 'item_index': 454, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_mpi_conf_unknownkeys', 'location': ('tests/test_mpi.py', 36, 'test_mpi_conf_unknownkeys'), 'keywords': {'test_mpi_conf_unknownkeys': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00024022699926717905, 'start': 1685951444.7648141, 'stop': 1685951444.765056, '$report_type': 'TestReport', 'item_index': 454, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::test_mpi_conf_unknownkeys - location: ('tests/test_mpi.py', 36, 'test_mpi_conf_unknownkeys') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::TestMpiRun::test_fake_mpi_config - location: ('tests/test_mpi.py', 128, 'TestMpiRun.test_fake_mpi_config') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_fake_mpi_config', 'location': ('tests/test_mpi.py', 128, 'TestMpiRun.test_fake_mpi_config'), 'keywords': {'test_fake_mpi_config': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0038759959998060367, 'start': 1685951444.766158, 'stop': 1685951444.770035, '$report_type': 'TestReport', 'item_index': 455, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_fake_mpi_config', 'location': ('tests/test_mpi.py', 128, 'TestMpiRun.test_fake_mpi_config'), 'keywords': {'test_fake_mpi_config': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.003570607000256132, 'start': 1685951444.770457, 'stop': 1685951444.774029, '$report_type': 'TestReport', 'item_index': 455, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_fake_mpi_config', 'location': ('tests/test_mpi.py', 128, 'TestMpiRun.test_fake_mpi_config'), 'keywords': {'test_fake_mpi_config': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0007795419996909914, 'start': 1685951444.774543, 'stop': 1685951444.7753248, '$report_type': 'TestReport', 'item_index': 455, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::TestMpiRun::test_fake_mpi_config - location: ('tests/test_mpi.py', 128, 'TestMpiRun.test_fake_mpi_config') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl] - location: ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]', 'location': ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]'), 'keywords': {'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/hello-workflow.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003464189994701883, 'start': 1685951444.776302, 'stop': 1685951444.77665, '$report_type': 'TestReport', 'item_index': 489, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_hint', 'location': ('tests/test_loop.py', 89, 'test_validate_loop_fail_on_hint'), 'keywords': {'test_validate_loop_fail_on_hint': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-hint.cwl:26:7: object id \'tests/loop/invalid-loop-hint.cwl#subworkflow/i1\' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mValidation failed at\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1048, in validate_hints\n raise ValidationException(\nschema_salad.exceptions.ValidationException: http://commonwl.org/cwltool#Loop is valid only under requirements.\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 107, in __init__\n self.make_workflow_step(step, index, loadingContext, loadingContext.prov_obj)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 152, in make_workflow_step\n return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 347, in __init__\n super().__init__(toolpath_object, loadingContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 603, in __init__\n self.validate_hints(\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1045, in validate_hints\n with sl:\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/sourceline.py", line 250, in __exit__\n raise self.makeError(str(exc_value)) from exc_value\nschema_salad.exceptions.ValidationException: tests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-hint.cwl:26:7: object id \'tests/loop/invalid-loop-hint.cwl#subworkflow/i1\' previously defined\nERROR cwltool:workflow.py:111 Validation failed at\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1048, in validate_hints\n raise ValidationException(\nschema_salad.exceptions.ValidationException: http://commonwl.org/cwltool#Loop is valid only under requirements.\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 107, in __init__\n self.make_workflow_step(step, index, loadingContext, loadingContext.prov_obj)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 152, in make_workflow_step\n return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 347, in __init__\n super().__init__(toolpath_object, loadingContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 603, in __init__\n self.validate_hints(\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1045, in validate_hints\n with sl:\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/sourceline.py", line 250, in __exit__\n raise self.makeError(str(exc_value)) from exc_value\nschema_salad.exceptions.ValidationException: tests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.')], 'duration': 0.8786398969996299, 'start': 1685951443.930252, 'stop': 1685951444.808871, '$report_type': 'TestReport', 'item_index': 426, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_validate_loop_fail_on_hint', 'location': ('tests/test_loop.py', 89, 'test_validate_loop_fail_on_hint'), 'keywords': {'test_validate_loop_fail_on_hint': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\'\nURI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-loop-hint.cwl:26:7: object id \'tests/loop/invalid-loop-hint.cwl#subworkflow/i1\' previously defined\n\x1b[1;30mERROR\x1b[0m \x1b[31mValidation failed at\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1048, in validate_hints\n raise ValidationException(\nschema_salad.exceptions.ValidationException: http://commonwl.org/cwltool#Loop is valid only under requirements.\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 107, in __init__\n self.make_workflow_step(step, index, loadingContext, loadingContext.prov_obj)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 152, in make_workflow_step\n return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 347, in __init__\n super().__init__(toolpath_object, loadingContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 603, in __init__\n self.validate_hints(\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1045, in validate_hints\n with sl:\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/sourceline.py", line 250, in __exit__\n raise self.makeError(str(exc_value)) from exc_value\nschema_salad.exceptions.ValidationException: tests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-loop-hint.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-loop-hint.cwl:26:7: object id \'tests/loop/invalid-loop-hint.cwl#subworkflow/i1\' previously defined\nERROR cwltool:workflow.py:111 Validation failed at\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1048, in validate_hints\n raise ValidationException(\nschema_salad.exceptions.ValidationException: http://commonwl.org/cwltool#Loop is valid only under requirements.\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 107, in __init__\n self.make_workflow_step(step, index, loadingContext, loadingContext.prov_obj)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 152, in make_workflow_step\n return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 347, in __init__\n super().__init__(toolpath_object, loadingContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 603, in __init__\n self.validate_hints(\n File "/Users/jasperk/gitlab/cwltool/cwltool/process.py", line 1045, in validate_hints\n with sl:\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/schema_salad/sourceline.py", line 250, in __exit__\n raise self.makeError(str(exc_value)) from exc_value\nschema_salad.exceptions.ValidationException: tests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/loop/invalid-loop-hint.cwl:29:7: http://commonwl.org/cwltool#Loop is valid only under\n requirements.')], 'duration': 0.0003478279995761113, 'start': 1685951444.8094342, 'stop': 1685951444.809783, '$report_type': 'TestReport', 'item_index': 426, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_validate_loop_fail_on_hint - location: ('tests/test_loop.py', 89, 'test_validate_loop_fail_on_hint') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_fail_non_boolean_loop_when', 'location': ('tests/test_loop.py', 99, 'test_loop_fail_non_boolean_loop_when'), 'keywords': {'test_loop_fail_non_boolean_loop_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00019406599949434167, 'start': 1685951444.8108952, 'stop': 1685951444.8110888, '$report_type': 'TestReport', 'item_index': 427, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_loop_fail_non_boolean_loop_when - location: ('tests/test_loop.py', 99, 'test_loop_fail_non_boolean_loop_when') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]', 'location': ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]'), 'keywords': {'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/hello-workflow.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'")], 'duration': 0.046458136000183003, 'start': 1685951444.777009, 'stop': 1685951444.823467, '$report_type': 'TestReport', 'item_index': 489, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]', 'location': ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]'), 'keywords': {'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/hello-workflow.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'")], 'duration': 0.00031945299997460097, 'start': 1685951444.8240378, 'stop': 1685951444.824359, '$report_type': 'TestReport', 'item_index': 489, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl] - location: ('tests/test_pack.py', 121, 'test_pack_missing_cwlVersion[tests/wf/hello-workflow.cwl]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_pack_idempotence_tool - location: ('tests/test_pack.py', 138, 'test_pack_idempotence_tool') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_idempotence_tool', 'location': ('tests/test_pack.py', 138, 'test_pack_idempotence_tool'), 'keywords': {'test_pack_idempotence_tool': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011834360002467292, 'start': 1685951444.825451, 'stop': 1685951444.826636, '$report_type': 'TestReport', 'item_index': 490, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_idempotence_tool', 'location': ('tests/test_pack.py', 138, 'test_pack_idempotence_tool'), 'keywords': {'test_pack_idempotence_tool': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_tool0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_tool0/packed.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_tool0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_tool0/packed.cwl'")], 'duration': 0.04199383000013768, 'start': 1685951444.827132, 'stop': 1685951444.8691258, '$report_type': 'TestReport', 'item_index': 490, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_pack_idempotence_tool - location: ('tests/test_pack.py', 138, 'test_pack_idempotence_tool') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_pack_idempotence_workflow - location: ('tests/test_pack.py', 143, 'test_pack_idempotence_workflow') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_idempotence_workflow', 'location': ('tests/test_pack.py', 143, 'test_pack_idempotence_workflow'), 'keywords': {'test_pack_idempotence_workflow': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0010339679993194295, 'start': 1685951444.870764, 'stop': 1685951444.871799, '$report_type': 'TestReport', 'item_index': 491, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] -",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$05b0c06f1a5d09cb506e00062429a2281b169cb6",\n "size": 24,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_expr.cwl] Removing input staging directory /private/tmp/docker_tmpuhnsmj7a\nDEBUG cwltool:job.py:454 [job mpi_expr.cwl] Removing temporary directory /private/tmp/docker_tmpubimcz5_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpaigw30gn/46516be4494917870bf55e45a1047abf0da9e0b8 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_simple_mpi_nproc_expr0/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaigw30gn\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1397649960008494, 'start': 1685951443.578856, 'stop': 1685951444.718595, '$report_type': 'TestReport', 'item_index': 457, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} -pŒmðŸX0±\0?SðŸX0?S0=Sð]]Ú§Xر3=S0¹Q°½Xð]]ðŸX°JT0^]0?S0§X°½XðwTð¦X0±\0^]ð]]0§X0§X0FTðªQð¦Xð#\ð]]°>S°Óm°ÄZ°>S°ÄZ°ÄZ°>S°dp^]0§X°½XðwTð¦X0±\°d0Œm0§X0?S0¹QðI^ð]]ð]]0Œm°d0§X°œQ°dðŸXðÙm0FT0±\°dp+_ptðŸXðÙm0FT0±\ptÚdšƒØ±±I^ðwTðwTðI^ðÙm809891'} -er.io/everpeace/curl-jq\']\nUsing default tag: latest\nlatest: Pulling from everpeace/curl-jq\nDigest: sha256:913ca8896b01799201a1eeb9ddf9 pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_passthrough_successive', 'location': ('tests/test_iwdr.py', 29, 'test_passthrough_successive'), 'keywords': {'test_passthrough_successive': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _2] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1 not ready\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step mkdirs\nDEBUG cwltool:workflow_job.py:727 [step mkdirs] job input {}\nDEBUG cwltool:workflow_job.py:732 [step mkdirs] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step mkdirs] start\nDEBUG cwltool:command_line_tool.py:982 [job mkdirs] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#mkdirs/2b25f995-b05d-4dcf-a9bc-f2418a66296d as part of step mkdirs\nDEBUG cwltool:command_line_tool.py:988 [job mkdirs] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mkdirs] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mkdirs] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "mkdir dir dir/subdir && touch dir/subdir/file"\n },\n {\n "position": [\n -1000000,\n 3\n ],\n "datum": "-"\n }\n]\nDEBUG cwltool:job.py:215 [job mkdirs] initial work dir {}\nINFO cwltool:job.py:266 [job mkdirs] /private/tmp/docker_tmpijyeq8bv$ bash \\\n -c \\\n \'mkdir dir dir/subdir && touch dir/subdir/file\' \\\n -\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mkdirs] completed success\nDEBUG cwltool:job.py:422 [job mkdirs] outputs {\n "mkdirs_out": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step mkdirs] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#mkdirs/mkdirs_out": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step mkdirs] completed success\nDEBUG cwltool:job.py:446 [job mkdirs] Removing input staging directory /private/tmp/docker_tmphrcu_ih1\nDEBUG cwltool:job.py:454 [job mkdirs] Removing temporary directory /private/tmp/docker_tmp_h9cg8p2\nDEBUG cwltool:workflow_job.py:610 [workflow _2] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2 not ready\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step passthrough1\nDEBUG cwltool:workflow_job.py:727 [step passthrough1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step passthrough1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:75 [step passthrough1] start\nDEBUG cwltool:command_line_tool.py:982 [job passthrough1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/7a196622-4d49-479f-a3b1-df60a7883de2 as part of step passthrough1\nDEBUG cwltool:command_line_tool.py:988 [job passthrough1] {\n "passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "basename": "file",\n "size": 0\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job passthrough1] path mappings is {\n "file:///private/tmp/docker_tmpijyeq8bv/dir": [\n "/private/tmp/docker_tmpijyeq8bv/dir",\n "/private/tmp/docker_tmpso0k9rfa/dir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir/file",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job passthrough1] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job passthrough1] initial work dir {\n "file:///private/tmp/docker_tmpijyeq8bv/dir": [\n "/private/tmp/docker_tmpijyeq8bv/dir",\n "/private/tmp/docker_tmpso0k9rfa/dir",\n "Directory",\n true\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir/file",\n "File",\n false\n ]\n}\nINFO cwltool:job.py:266 [job passthrough1] /private/tmp/docker_tmpso0k9rfa$ true\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job passthrough1] completed success\nDEBUG cwltool:job.py:422 [job passthrough1] outputs {\n "passthrough1_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step passthrough1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step passthrough1] completed success\nDEBUG cwltool:job.py:446 [job passthrough1] Removing input staging directory /private/tmp/docker_tmpg2ol4k_l\nDEBUG cwltool:job.py:454 [job passthrough1] Removing temporary directory /private/tmp/docker_tmpm9x2m7gy\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step passthrough2\nDEBUG cwltool:workflow_job.py:727 [step passthrough2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step passthrough2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:75 [step passthrough2] start\nDEBUG cwltool:command_line_tool.py:982 [job passthrough2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/fab92b9c-ed66-45ae-ae7f-411f0edd6009 as part of step passthrough2\nDEBUG cwltool:command_line_tool.py:988 [job passthrough2] {\n "passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "basename": "file",\n "size": 0\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job passthrough2] path mappings is {\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmp1p6du01p/subdir",\n "Directory",\n false\n ],\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmp1p6du01p/subdir/file",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job passthrough2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job passthrough2] initial work dir {\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmp1p6du01p/subdir",\n "Directory",\n true\n ],\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmp1p6du01p/subdir/file",\n "File",\n true\n ]\n}\nINFO cwltool:job.py:266 [job passthrough2] /private/tmp/docker_tmp1p6du01p$ true\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job passthrough2] completed success\nDEBUG cwltool:job.py:422 [job passthrough2] outputs {\n "passthrough2_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step passthrough2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step passthrough2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {\n "out": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job passthrough2] Removing input staging directory /private/tmp/docker_tmpjmoq_pe2\nDEBUG cwltool:job.py:454 [job passthrough2] Removing temporary directory /private/tmp/docker_tmp1dce8v2z\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpijyeq8bv/dir/subdir to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw0/test_passthrough_successive0/subdir\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1p6du01p\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa3js7lcr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpso0k9rfa\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpijyeq8bv\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.778309483999692, 'start': 1685951444.1388621, 'stop': 1685951444.917154, '$report_type': 'TestReport', 'item_index': 393, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_iwdr.py::test_passthrough_successive', 'location': ('tests/test_iwdr.py', 29, 'test_passthrough_successive'), 'keywords': {'test_passthrough_successive': 1, 'test_iwdr.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _2] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1 not ready\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step mkdirs\nDEBUG cwltool:workflow_job.py:727 [step mkdirs] job input {}\nDEBUG cwltool:workflow_job.py:732 [step mkdirs] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step mkdirs] start\nDEBUG cwltool:command_line_tool.py:982 [job mkdirs] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#mkdirs/2b25f995-b05d-4dcf-a9bc-f2418a66296d as part of step mkdirs\nDEBUG cwltool:command_line_tool.py:988 [job mkdirs] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mkdirs] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mkdirs] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "mkdir dir dir/subdir && touch dir/subdir/file"\n },\n {\n "position": [\n -1000000,\n 3\n ],\n "datum": "-"\n }\n]\nDEBUG cwltool:job.py:215 [job mkdirs] initial work dir {}\nINFO cwltool:job.py:266 [job mkdirs] /private/tmp/docker_tmpijyeq8bv$ bash \\\n -c \\\n \'mkdir dir dir/subdir && touch dir/subdir/file\' \\\n -\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mkdirs] completed success\nDEBUG cwltool:job.py:422 [job mkdirs] outputs {\n "mkdirs_out": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step mkdirs] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#mkdirs/mkdirs_out": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step mkdirs] completed success\nDEBUG cwltool:job.py:446 [job mkdirs] Removing input staging directory /private/tmp/docker_tmphrcu_ih1\nDEBUG cwltool:job.py:454 [job mkdirs] Removing temporary directory /private/tmp/docker_tmp_h9cg8p2\nDEBUG cwltool:workflow_job.py:610 [workflow _2] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2 not ready\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step passthrough1\nDEBUG cwltool:workflow_job.py:727 [step passthrough1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step passthrough1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:75 [step passthrough1] start\nDEBUG cwltool:command_line_tool.py:982 [job passthrough1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/7a196622-4d49-479f-a3b1-df60a7883de2 as part of step passthrough1\nDEBUG cwltool:command_line_tool.py:988 [job passthrough1] {\n "passthrough1_in": {\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir",\n "basename": "dir",\n "nameroot": "dir",\n "nameext": "",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "basename": "file",\n "size": 0\n }\n ]\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job passthrough1] path mappings is {\n "file:///private/tmp/docker_tmpijyeq8bv/dir": [\n "/private/tmp/docker_tmpijyeq8bv/dir",\n "/private/tmp/docker_tmpso0k9rfa/dir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir/file",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job passthrough1] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job passthrough1] initial work dir {\n "file:///private/tmp/docker_tmpijyeq8bv/dir": [\n "/private/tmp/docker_tmpijyeq8bv/dir",\n "/private/tmp/docker_tmpso0k9rfa/dir",\n "Directory",\n true\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir",\n "Directory",\n false\n ],\n "file:///private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmpso0k9rfa/dir/subdir/file",\n "File",\n false\n ]\n}\nINFO cwltool:job.py:266 [job passthrough1] /private/tmp/docker_tmpso0k9rfa$ true\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job passthrough1] completed success\nDEBUG cwltool:job.py:422 [job passthrough1] outputs {\n "passthrough1_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step passthrough1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough1/passthrough1_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step passthrough1] completed success\nDEBUG cwltool:job.py:446 [job passthrough1] Removing input staging directory /private/tmp/docker_tmpg2ol4k_l\nDEBUG cwltool:job.py:454 [job passthrough1] Removing temporary directory /private/tmp/docker_tmpm9x2m7gy\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step passthrough2\nDEBUG cwltool:workflow_job.py:727 [step passthrough2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step passthrough2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:75 [step passthrough2] start\nDEBUG cwltool:command_line_tool.py:982 [job passthrough2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/fab92b9c-ed66-45ae-ae7f-411f0edd6009 as part of step passthrough2\nDEBUG cwltool:command_line_tool.py:988 [job passthrough2] {\n "passthrough2_in": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "basename": "file",\n "size": 0\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job passthrough2] path mappings is {\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmp1p6du01p/subdir",\n "Directory",\n false\n ],\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmp1p6du01p/subdir/file",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job passthrough2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job passthrough2] initial work dir {\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "/private/tmp/docker_tmp1p6du01p/subdir",\n "Directory",\n true\n ],\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file": [\n "/private/tmp/docker_tmpijyeq8bv/dir/subdir/file",\n "/private/tmp/docker_tmp1p6du01p/subdir/file",\n "File",\n true\n ]\n}\nINFO cwltool:job.py:266 [job passthrough2] /private/tmp/docker_tmp1p6du01p$ true\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job passthrough2] completed success\nDEBUG cwltool:job.py:422 [job passthrough2] outputs {\n "passthrough2_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step passthrough2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-passthrough-successive.cwl#passthrough2/passthrough2_subdir": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nINFO cwltool:workflow_job.py:572 [step passthrough2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _2] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {\n "out": {\n "location": "/private/tmp/docker_tmpijyeq8bv/dir/subdir",\n "basename": "subdir",\n "nameroot": "subdir",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job passthrough2] Removing input staging directory /private/tmp/docker_tmpjmoq_pe2\nDEBUG cwltool:job.py:454 [job passthrough2] Removing temporary directory /private/tmp/docker_tmp1dce8v2z\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpijyeq8bv/dir/subdir to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw0/test_passthrough_successive0/subdir\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1p6du01p\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpa3js7lcr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpso0k9rfa\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpijyeq8bv\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005935129993304145, 'start': 1685951444.918226, 'stop': 1685951444.918821, '$report_type': 'TestReport', 'item_index': 393, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_iwdr.py::test_passthrough_successive - location: ('tests/test_iwdr.py', 29, 'test_passthrough_successive') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.] - location: ('tests/test_override.py', 119, "test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]") - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007491690003007534, 'start': 1685951444.920224, 'stop': 1685951444.920974, '$report_type': 'TestReport', 'item_index': 479, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_idempotence_workflow', 'location': ('tests/test_pack.py', 143, 'test_pack_idempotence_workflow'), 'keywords': {'test_pack_idempotence_workflow': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl'")], 'duration': 0.16907998900023813, 'start': 1685951444.8721511, 'stop': 1685951445.041229, '$report_type': 'TestReport', 'item_index': 491, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_idempotence_workflow', 'location': ('tests/test_pack.py', 143, 'test_pack_idempotence_workflow'), 'keywords': {'test_pack_idempotence_workflow': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\n\x1b[32m[2023-06-05 09:50:44]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl'\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_pack_idempotence_workflow0/packed.cwl'")], 'duration': 0.0005268760005492368, 'start': 1685951445.041944, 'stop': 1685951445.042474, '$report_type': 'TestReport', 'item_index': 491, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_pack_idempotence_workflow - location: ('tests/test_pack.py', 143, 'test_pack_idempotence_workflow') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False] - location: ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]'), 'keywords': {'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015690330001234543, 'start': 1685951445.043638, 'stop': 1685951445.045208, '$report_type': 'TestReport', 'item_index': 492, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters1-result1]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters1-result1]'), 'keywords': {'test_overrides[parameters1-result1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters1-result1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_3] /private/tmp/docker_tmpzeavrjm9$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpzeavrjm9/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_3] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_3] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_3] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_3] /private/tmp/docker_tmpzeavrjm9$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpzeavrjm9/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_3] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_3] Removing input staging directory /private/tmp/docker_tmpu4_tqu0y\nDEBUG cwltool:job.py:454 [job echo.cwl_3] Removing temporary directory /private/tmp/docker_tmpij4rzbsm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzeavrjm9\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7023725059998469, 'start': 1685951444.456256, 'stop': 1685951445.158613, '$report_type': 'TestReport', 'item_index': 468, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters1-result1]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters1-result1]'), 'keywords': {'test_overrides[parameters1-result1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters1-result1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_3] /private/tmp/docker_tmpzeavrjm9$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpzeavrjm9/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_3] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_3] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_3] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_3] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_3] /private/tmp/docker_tmpzeavrjm9$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpzeavrjm9/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_3] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_3] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_3] Removing input staging directory /private/tmp/docker_tmpu4_tqu0y\nDEBUG cwltool:job.py:454 [job echo.cwl_3] Removing temporary directory /private/tmp/docker_tmpij4rzbsm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzeavrjm9\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0012532579994513071, 'start': 1685951445.160028, 'stop': 1685951445.1612842, '$report_type': 'TestReport', 'item_index': 468, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides[parameters1-result1] - location: ('tests/test_override.py', 76, 'test_overrides[parameters1-result1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides[parameters2-result2] - location: ('tests/test_override.py', 76, 'test_overrides[parameters2-result2]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters2-result2]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters2-result2]'), 'keywords': {'test_overrides[parameters2-result2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-result2': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001179238999611698, 'start': 1685951445.1633039, 'stop': 1685951445.1644852, '$report_type': 'TestReport', 'item_index': 469, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nVersion 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.")], 'duration': 0.7835435590004636, 'start': 1685951444.921406, 'stop': 1685951445.7049322, '$report_type': 'TestReport', 'item_index': 479, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nVersion 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.")], 'duration': 0.0006185950005601626, 'start': 1685951445.7059588, 'stop': 1685951445.70658, '$report_type': 'TestReport', 'item_index': 479, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.] - location: ('tests/test_override.py', 119, "test_overrides_fails[parameters3-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl] - location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort.cwl-tests/wf/expect_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005526220002138871, 'start': 1685951445.708649, 'stop': 1685951445.709203, '$report_type': 'TestReport', 'item_index': 480, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_fail_non_boolean_loop_when', 'location': ('tests/test_loop.py', 99, 'test_loop_fail_non_boolean_loop_when'), 'keywords': {'test_loop_fail_non_boolean_loop_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "o1": null\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-non-boolean-loopWhen.cwl:32:11: object id 'tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _12] start\n\x1b[1;30mINFO\x1b[0m [workflow _12] starting step subworkflow\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step subworkflow] Cannot make job: Loop condition 'loopWhen' must evaluate to 'true' or 'false'\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _12] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-non-boolean-loopWhen.cwl:32:11: object id \'tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step subworkflow\nDEBUG cwltool:workflow_job.py:727 [step subworkflow] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i2": 1\n}\nERROR cwltool:workflow_job.py:833 [step subworkflow] Cannot make job: Loop condition \'loopWhen\' must evaluate to \'true\' or \'false\'\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 751, in try_make_job\n yield from jobs\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 936, in job\n raise WorkflowException(\ncwltool.errors.WorkflowException: Loop condition \'loopWhen\' must evaluate to \'true\' or \'false\'\nINFO cwltool:workflow_job.py:539 [workflow _12] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {\n "o1": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbnn_geot\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.9484818880000603, 'start': 1685951444.811543, 'stop': 1685951445.7600021, '$report_type': 'TestReport', 'item_index': 427, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_fail_non_boolean_loop_when', 'location': ('tests/test_loop.py', 99, 'test_loop_fail_non_boolean_loop_when'), 'keywords': {'test_loop_fail_non_boolean_loop_when': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "o1": null\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/invalid-non-boolean-loopWhen.cwl:32:11: object id 'tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _12] start\n\x1b[1;30mINFO\x1b[0m [workflow _12] starting step subworkflow\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step subworkflow] Cannot make job: Loop condition 'loopWhen' must evaluate to 'true' or 'false'\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _12] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/invalid-non-boolean-loopWhen.cwl:32:11: object id \'tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step subworkflow\nDEBUG cwltool:workflow_job.py:727 [step subworkflow] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/invalid-non-boolean-loopWhen.cwl#subworkflow/i2": 1\n}\nERROR cwltool:workflow_job.py:833 [step subworkflow] Cannot make job: Loop condition \'loopWhen\' must evaluate to \'true\' or \'false\'\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 751, in try_make_job\n yield from jobs\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 936, in job\n raise WorkflowException(\ncwltool.errors.WorkflowException: Loop condition \'loopWhen\' must evaluate to \'true\' or \'false\'\nINFO cwltool:workflow_job.py:539 [workflow _12] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {\n "o1": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbnn_geot\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.000542493000466493, 'start': 1685951445.7606468, 'stop': 1685951445.761191, '$report_type': 'TestReport', 'item_index': 427, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_loop_fail_non_boolean_loop_when - location: ('tests/test_loop.py', 99, 'test_loop_fail_non_boolean_loop_when') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_loop_single_variable - location: ('tests/test_loop.py', 109, 'test_loop_single_variable') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable', 'location': ('tests/test_loop.py', 109, 'test_loop_single_variable'), 'keywords': {'test_loop_single_variable': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00030629299999418436, 'start': 1685951445.762482, 'stop': 1685951445.76279, '$report_type': 'TestReport', 'item_index': 428, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters2-result2]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters2-result2]'), 'keywords': {'test_overrides[parameters2-result2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-result2': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_4] /private/tmp/docker_tmp8c1vt_no$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp8c1vt_no/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_4] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_4] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_4] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_4] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_4] /private/tmp/docker_tmp8c1vt_no$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp8c1vt_no/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_4] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_4] outputs {\n "out": "zing hello3\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_4] Removing input staging directory /private/tmp/docker_tmp0re0kkyy\nDEBUG cwltool:job.py:454 [job echo.cwl_4] Removing temporary directory /private/tmp/docker_tmptk7mihrz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp8c1vt_no\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.71063700600007, 'start': 1685951445.165343, 'stop': 1685951445.8759658, '$report_type': 'TestReport', 'item_index': 469, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters2-result2]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters2-result2]'), 'keywords': {'test_overrides[parameters2-result2]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-result2': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_4] /private/tmp/docker_tmp8c1vt_no$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp8c1vt_no/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_4] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_4] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_4] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_4] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_4] /private/tmp/docker_tmp8c1vt_no$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp8c1vt_no/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_4] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_4] outputs {\n "out": "zing hello3\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_4] Removing input staging directory /private/tmp/docker_tmp0re0kkyy\nDEBUG cwltool:job.py:454 [job echo.cwl_4] Removing temporary directory /private/tmp/docker_tmptk7mihrz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp8c1vt_no\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007379569997283397, 'start': 1685951445.8771148, 'stop': 1685951445.877855, '$report_type': 'TestReport', 'item_index': 469, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides[parameters2-result2] - location: ('tests/test_override.py', 76, 'test_overrides[parameters2-result2]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides[parameters3-result3] - location: ('tests/test_override.py', 76, 'test_overrides[parameters3-result3]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters3-result3]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters3-result3]'), 'keywords': {'test_overrides[parameters3-result3]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters3-result3': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008628899995528627, 'start': 1685951445.879502, 'stop': 1685951445.880367, '$report_type': 'TestReport', 'item_index': 470, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_mpi_workflow', 'location': ('tests/test_mpi.py', 174, 'TestMpiRun.test_mpi_workflow'), 'keywords': {'test_mpi_workflow': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "processes": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step par_pids\nDEBUG cwltool:workflow_job.py:727 [step par_pids] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/processes": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step par_pids] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/processes": 3\n}\nINFO cwltool:workflow_job.py:75 [step par_pids] start\nDEBUG cwltool:command_line_tool.py:982 [job par_pids] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl as part of step par_pids\nDEBUG cwltool:command_line_tool.py:988 [job par_pids] {\n "processes": 3\n}\nDEBUG cwltool:command_line_tool.py:1000 [job par_pids] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job par_pids] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job par_pids] initial work dir {}\nINFO cwltool:job.py:266 [job par_pids] /private/tmp/docker_tmp85u5ffmq$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 3 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job par_pids] completed success\nDEBUG cwltool:job.py:422 [job par_pids] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step par_pids] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/pids": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step par_pids] completed success\nDEBUG cwltool:job.py:446 [job par_pids] Removing input staging directory /private/tmp/docker_tmppt3kvz7k\nDEBUG cwltool:job.py:454 [job par_pids] Removing temporary directory /private/tmp/docker_tmpc8nr7b2m\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step count\nDEBUG cwltool:workflow_job.py:727 [step count] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step count] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step count] start\nDEBUG cwltool:command_line_tool.py:982 [job count] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_line_count.cwl as part of step count\nDEBUG cwltool:command_line_tool.py:988 [job count] {\n "pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count] path mappings is {\n "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8": [\n "/private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "/private/tmp/docker_tmp7lqo6r6u/stg2cb31d92-a49d-40a8-b109-fcc66ba5559b/46516be4494917870bf55e45a1047abf0da9e0b8",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count] initial work dir {}\nINFO cwltool:job.py:266 [job count] /private/tmp/docker_tmp6x96v1_p$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 1 \\\n --no-fail \\\n wc \\\n -l < /private/tmp/docker_tmp7lqo6r6u/stg2cb31d92-a49d-40a8-b109-fcc66ba5559b/46516be4494917870bf55e45a1047abf0da9e0b8 > /private/tmp/docker_tmp6x96v1_p/line_count\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job count] completed success\nDEBUG cwltool:job.py:422 [job count] outputs {\n "line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step count] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step count] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count] Removing input staging directory /private/tmp/docker_tmp7lqo6r6u\nDEBUG cwltool:job.py:454 [job count] Removing temporary directory /private/tmp/docker_tmp4b2tpt7w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6x96v1_p/line_count to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_mpi_workflow0/line_count\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp85u5ffmq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpne46mazt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6x96v1_p\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.3001793530002033, 'start': 1685951444.7247481, 'stop': 1685951446.024896, '$report_type': 'TestReport', 'item_index': 458, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_mpi_workflow', 'location': ('tests/test_mpi.py', 174, 'TestMpiRun.test_mpi_workflow'), 'keywords': {'test_mpi_workflow': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "processes": 3\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step par_pids\nDEBUG cwltool:workflow_job.py:727 [step par_pids] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/processes": 3\n}\nDEBUG cwltool:workflow_job.py:732 [step par_pids] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/processes": 3\n}\nINFO cwltool:workflow_job.py:75 [step par_pids] start\nDEBUG cwltool:command_line_tool.py:982 [job par_pids] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_expr.cwl as part of step par_pids\nDEBUG cwltool:command_line_tool.py:988 [job par_pids] {\n "processes": 3\n}\nDEBUG cwltool:command_line_tool.py:1000 [job par_pids] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job par_pids] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "import os; print(os.getpid())"\n }\n]\nDEBUG cwltool:job.py:215 [job par_pids] initial work dir {}\nINFO cwltool:job.py:266 [job par_pids] /private/tmp/docker_tmp85u5ffmq$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 3 \\\n --no-fail \\\n python \\\n -c \\\n \'import os; print(os.getpid())\' > /private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job par_pids] completed success\nDEBUG cwltool:job.py:422 [job par_pids] outputs {\n "pids": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step par_pids] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#par_pids/pids": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step par_pids] completed success\nDEBUG cwltool:job.py:446 [job par_pids] Removing input staging directory /private/tmp/docker_tmppt3kvz7k\nDEBUG cwltool:job.py:454 [job par_pids] Removing temporary directory /private/tmp/docker_tmpc8nr7b2m\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step count\nDEBUG cwltool:workflow_job.py:727 [step count] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step count] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step count] start\nDEBUG cwltool:command_line_tool.py:982 [job count] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_line_count.cwl as part of step count\nDEBUG cwltool:command_line_tool.py:988 [job count] {\n "pid_file": {\n "location": "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "basename": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameroot": "46516be4494917870bf55e45a1047abf0da9e0b8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6bb1f24b4bc5cfde090fd13767d1e87dde2060fa",\n "size": 18,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count] path mappings is {\n "file:///private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8": [\n "/private/tmp/docker_tmp85u5ffmq/46516be4494917870bf55e45a1047abf0da9e0b8",\n "/private/tmp/docker_tmp7lqo6r6u/stg2cb31d92-a49d-40a8-b109-fcc66ba5559b/46516be4494917870bf55e45a1047abf0da9e0b8",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count] initial work dir {}\nINFO cwltool:job.py:266 [job count] /private/tmp/docker_tmp6x96v1_p$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 1 \\\n --no-fail \\\n wc \\\n -l < /private/tmp/docker_tmp7lqo6r6u/stg2cb31d92-a49d-40a8-b109-fcc66ba5559b/46516be4494917870bf55e45a1047abf0da9e0b8 > /private/tmp/docker_tmp6x96v1_p/line_count\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job count] completed success\nDEBUG cwltool:job.py:422 [job count] outputs {\n "line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step count] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_simple_wf.cwl#count/line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step count] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "line_count": {\n "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count",\n "basename": "line_count",\n "nameroot": "line_count",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbf4852f",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count] Removing input staging directory /private/tmp/docker_tmp7lqo6r6u\nDEBUG cwltool:job.py:454 [job count] Removing temporary directory /private/tmp/docker_tmp4b2tpt7w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6x96v1_p/line_count to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_mpi_workflow0/line_count\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp85u5ffmq\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpne46mazt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6x96v1_p\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006665989994871779, 'start': 1685951446.0263638, 'stop': 1685951446.0270321, '$report_type': 'TestReport', 'item_index': 458, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::TestMpiRun::test_mpi_workflow - location: ('tests/test_mpi.py', 174, 'TestMpiRun.test_mpi_workflow') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::TestMpiRun::test_environment - location: ('tests/test_mpi.py', 194, 'TestMpiRun.test_environment') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_environment', 'location': ('tests/test_mpi.py', 194, 'TestMpiRun.test_environment'), 'keywords': {'test_environment': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001445703000172216, 'start': 1685951446.028768, 'stop': 1685951446.030216, '$report_type': 'TestReport', 'item_index': 459, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort.cwl-tests/wf/expect_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:45]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'")], 'duration': 0.7957583910001631, 'start': 1685951445.709607, 'stop': 1685951446.505347, '$report_type': 'TestReport', 'item_index': 480, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort.cwl-tests/wf/expect_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:45]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'")], 'duration': 0.00042291299996577436, 'start': 1685951446.506038, 'stop': 1685951446.5064619, '$report_type': 'TestReport', 'item_index': 480, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl] - location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort.cwl-tests/wf/expect_packed.cwl]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl] - location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]'), 'keywords': {'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006471120004789555, 'start': 1685951446.507751, 'stop': 1685951446.508399, '$report_type': 'TestReport', 'item_index': 481, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_write_write_conflict', 'location': ('tests/test_ext.py', 207, 'test_write_write_conflict'), 'keywords': {'test_write_write_conflict': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m [workflow _2] start\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step step2_2\n\x1b[1;30mINFO\x1b[0m [step step2_2] start\n\x1b[1;30mINFO\x1b[0m [job step2_2] /private/tmp/docker_tmpptsgalmt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpptsgalmt,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp4qbnegg7,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmhfpqlte/20230605095045-609224.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step2_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mERROR\x1b[0m \x1b[31mException on step 'step1'\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step step1_2] Cannot make job: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _2] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl",\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value"\n }\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step step2_2\nDEBUG cwltool:workflow_job.py:727 [step step2_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step2/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step2/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step2_2\nDEBUG cwltool:command_line_tool.py:988 [job step2_2] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step2_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step2_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job step2_2] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step2_2] /private/tmp/docker_tmpptsgalmt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpptsgalmt,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp4qbnegg7,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmhfpqlte/20230605095045-609224.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step2_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step2_2] completed success\nDEBUG cwltool:job.py:422 [job step2_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpptsgalmt/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_2] produced output {}\nINFO cwltool:workflow_job.py:572 [step step2_2] completed success\nDEBUG cwltool:job.py:446 [job step2_2] Removing input staging directory /private/tmp/docker_tmpi7dfk_9x\nDEBUG cwltool:job.py:454 [job step2_2] Removing temporary directory /private/tmp/docker_tmp4qbnegg7\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgef2bfe92-5a62-4b36-b8ec-96b99ea4527f/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nERROR cwltool:workflow.py:465 Exception on step \'step1\'\nERROR cwltool:workflow_job.py:833 [step step1_2] Cannot make job: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 751, in try_make_job\n yield from jobs\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 77, in job\n yield from self.step.job(joborder, output_callback, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 459, in job\n yield from self.embedded_tool.job(\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 1090, in job\n adjustFileObjs(li, register_mut)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 273, in adjustFileObjs\n visit_class(rec, ("File",), op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 1080, in register_mut\n mm.register_mutation(j.name, f)\n File "/Users/jasperk/gitlab/cwltool/cwltool/mutation.py", line 69, in register_mutation\n raise WorkflowException(\ncwltool.errors.WorkflowException: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\nINFO cwltool:workflow_job.py:539 [workflow _2] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpptsgalmt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwij4jvx9\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 2.6720536889997675, 'start': 1685951443.967964, 'stop': 1685951446.6399539, '$report_type': 'TestReport', 'item_index': 374, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_write_write_conflict', 'location': ('tests/test_ext.py', 207, 'test_write_write_conflict'), 'keywords': {'test_write_write_conflict': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n\x1b[1;30mINFO\x1b[0m [workflow _2] start\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step step2_2\n\x1b[1;30mINFO\x1b[0m [step step2_2] start\n\x1b[1;30mINFO\x1b[0m [job step2_2] /private/tmp/docker_tmpptsgalmt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpptsgalmt,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp4qbnegg7,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmhfpqlte/20230605095045-609224.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py \\\n value\n\x1b[1;30mINFO\x1b[0m [job step2_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _2] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mERROR\x1b[0m \x1b[31mException on step 'step1'\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31m[step step1_2] Cannot make job: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _2] completed permanentFail\n\x1b[1;30mWARNING\x1b[0m \x1b[33mFinal process status is permanentFail\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl",\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value"\n }\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _2] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl\nINFO cwltool:workflow_job.py:765 [workflow _2] start\nDEBUG cwltool:workflow_job.py:777 [workflow _2] inputs {\n "a": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step step2_2\nDEBUG cwltool:workflow_job.py:727 [step step2_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step2/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step2/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step2_2\nDEBUG cwltool:command_line_tool.py:988 [job step2_2] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step2_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step2_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nDEBUG cwltool:job.py:215 [job step2_2] initial work dir {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step2_2] /private/tmp/docker_tmpptsgalmt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpptsgalmt,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp4qbnegg7,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py,target=/var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value,target=/hPkhbA/value \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpmhfpqlte/20230605095045-609224.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n /var/lib/cwl/stg712e7473-a718-466c-aab7-fdc32ec036ca/updateval.py \\\n value\nINFO cwltool:job.py:905 [job step2_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step2_2] completed success\nDEBUG cwltool:job.py:422 [job step2_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpptsgalmt/value",\n "basename": "value",\n "nameroot": "value",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da4b9237bacccdf19c0760cab7aec4a8359010b0",\n "size": 1,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_2] produced output {}\nINFO cwltool:workflow_job.py:572 [step step2_2] completed success\nDEBUG cwltool:job.py:446 [job step2_2] Removing input staging directory /private/tmp/docker_tmpi7dfk_9x\nDEBUG cwltool:job.py:454 [job step2_2] Removing temporary directory /private/tmp/docker_tmp4qbnegg7\nINFO cwltool:workflow_job.py:613 [workflow _2] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/mut.cwl#step1/r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval_inplace.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "r": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "size": 1,\n "basename": "value",\n "nameroot": "value",\n "nameext": ""\n },\n "script": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "basename": "updateval.py",\n "nameroot": "updateval",\n "nameext": ".py",\n "size": 102\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value",\n "/hPkhbA/value",\n "WritableFile",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/updateval.py": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/updateval.py",\n "/var/lib/cwl/stgef2bfe92-5a62-4b36-b8ec-96b99ea4527f/updateval.py",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.script)"\n },\n {\n "position": [\n 0,\n 2\n ],\n "valueFrom": "$(inputs.r.basename)"\n }\n]\nERROR cwltool:workflow.py:465 Exception on step \'step1\'\nERROR cwltool:workflow_job.py:833 [step step1_2] Cannot make job: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\nDEBUG cwltool:workflow_job.py:834 \nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 821, in job\n for newjob in step.iterable:\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 751, in try_make_job\n yield from jobs\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow_job.py", line 77, in job\n yield from self.step.job(joborder, output_callback, runtimeContext)\n File "/Users/jasperk/gitlab/cwltool/cwltool/workflow.py", line 459, in job\n yield from self.embedded_tool.job(\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 1090, in job\n adjustFileObjs(li, register_mut)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 273, in adjustFileObjs\n visit_class(rec, ("File",), op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 1080, in register_mut\n mm.register_mutation(j.name, f)\n File "/Users/jasperk/gitlab/cwltool/cwltool/mutation.py", line 69, in register_mutation\n raise WorkflowException(\ncwltool.errors.WorkflowException: [job step1_2] wants to modify file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_write_write_conflict0/value from generation 0 but current generation is 1 (last updated by step2_2)\nINFO cwltool:workflow_job.py:539 [workflow _2] completed permanentFail\nDEBUG cwltool:workflow_job.py:541 [workflow _2] outputs {}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpptsgalmt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwij4jvx9\nWARNING cwltool:main.py:1364 Final process status is permanentFail')], 'duration': 0.0014760510002815863, 'start': 1685951446.6416798, 'stop': 1685951446.6431592, '$report_type': 'TestReport', 'item_index': 374, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_write_write_conflict - location: ('tests/test_ext.py', 207, 'test_write_write_conflict') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_ext.py::test_read_write_conflict - location: ('tests/test_ext.py', 224, 'test_read_write_conflict') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_read_write_conflict', 'location': ('tests/test_ext.py', 224, 'test_read_write_conflict'), 'keywords': {'test_read_write_conflict': 1, 'skip': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_ext.py', 225, 'Skipped: This test is non-deterministic'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00024330199994437862, 'start': 1685951446.6445491, 'stop': 1685951446.644793, '$report_type': 'TestReport', 'item_index': 375, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_read_write_conflict', 'location': ('tests/test_ext.py', 224, 'test_read_write_conflict'), 'keywords': {'test_read_write_conflict': 1, 'skip': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0001879559995359159, 'start': 1685951446.64551, 'stop': 1685951446.645699, '$report_type': 'TestReport', 'item_index': 375, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_read_write_conflict - location: ('tests/test_ext.py', 224, 'test_read_write_conflict') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_require_prefix_networkaccess', 'location': ('tests/test_ext.py', 234, 'test_require_prefix_networkaccess'), 'keywords': {'test_require_prefix_networkaccess': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00022061199979361845, 'start': 1685951446.6465101, 'stop': 1685951446.646732, '$report_type': 'TestReport', 'item_index': 376, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_ext.py::test_require_prefix_networkaccess - location: ('tests/test_ext.py', 234, 'test_require_prefix_networkaccess') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters3-result3]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters3-result3]'), 'keywords': {'test_overrides[parameters3-result3]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters3-result3': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_5] /private/tmp/docker_tmp86l4ox2u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp86l4ox2u/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_5] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml",\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_5] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_5] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_5] /private/tmp/docker_tmp86l4ox2u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp86l4ox2u/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_5] outputs {\n "out": "zing hello4\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_5] Removing input staging directory /private/tmp/docker_tmp_n9ao4j7\nDEBUG cwltool:job.py:454 [job echo.cwl_5] Removing temporary directory /private/tmp/docker_tmpvsxoha6w\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp86l4ox2u\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.81195076899985, 'start': 1685951445.8809862, 'stop': 1685951446.692918, '$report_type': 'TestReport', 'item_index': 470, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters3-result3]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters3-result3]'), 'keywords': {'test_overrides[parameters3-result3]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters3-result3': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_5] /private/tmp/docker_tmp86l4ox2u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp86l4ox2u/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_5] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/override/echo-job-ov2.yml",\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_5] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_5] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_5] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_5] /private/tmp/docker_tmp86l4ox2u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmp86l4ox2u/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_5] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_5] outputs {\n "out": "zing hello4\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_5] Removing input staging directory /private/tmp/docker_tmp_n9ao4j7\nDEBUG cwltool:job.py:454 [job echo.cwl_5] Removing temporary directory /private/tmp/docker_tmpvsxoha6w\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp86l4ox2u\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000732627999241231, 'start': 1685951446.694444, 'stop': 1685951446.695177, '$report_type': 'TestReport', 'item_index': 470, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides[parameters3-result3] - location: ('tests/test_override.py', 76, 'test_overrides[parameters3-result3]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides[parameters4-result4] - location: ('tests/test_override.py', 76, 'test_overrides[parameters4-result4]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters4-result4]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters4-result4]'), 'keywords': {'test_overrides[parameters4-result4]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters4-result4': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.000645279999844206, 'start': 1685951446.696661, 'stop': 1685951446.6973069, '$report_type': 'TestReport', 'item_index': 471, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable', 'location': ('tests/test_loop.py', 109, 'test_loop_single_variable'), 'keywords': {'test_loop_single_variable': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _13] start\n\x1b[1;30mINFO\x1b[0m [workflow _13] starting step subworkflow_2\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _13] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop.cwl:26:7: object id \'tests/loop/single-var-loop.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step subworkflow_2\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/i1": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_2] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_2] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_2] inputs was {\n "i1": 10\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpyl41gacq\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0283650020001005, 'start': 1685951445.763399, 'stop': 1685951446.79174, '$report_type': 'TestReport', 'item_index': 428, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> -INFO 3.1 -INFO Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' -URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section? -tests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined -INFO [workflow _13] start -INFO [workflow _13] starting step subworkflow_2 -INFO [step subworkflow_2] start -INFO [step subworkflow_2] Iteration 1 completed success -INFO [step subworkflow_2] start -INFO [step subworkflow_2] Iteration 2 completed success -INFO [step subworkflow_2] start -INFO [step subworkflow_2] Iteration 3 completed success -INFO [step subworkflow_2] start -INFO [step subworkflow_2] Iteration 4 completed success -INFO [step subworkflow_2] start -INFO [step subworkflow_2] Iteration 5 completed success -INFO [step subworkflow_2] start -INFO [step subworkflow_2] Iteration 6 completed success -INFO [step subworkflow_2] start -INFO [step subworkflow_2] Iteration 7 completed success -INFO [step subworkflow_2] start -INFO [step subworkflow_2] Iteration 8 completed success -INFO [step subworkflow_2] start -INFO [step subworkflow_2] Iteration 9 completed success -INFO [step subworkflow_2] completed success -INFO [workflow _13] completed success -INFO Final process status is success -@PFNCaptured log callNyINFO cwltool:main.py:1027 3.1 -INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl' -WARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section? -WARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop.cwl:26:7: object id 'tests/loop/single-var-loop.cwl#subworkflow/i1' previously defined -DEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl -INFO cwltool:workflow_job.py:765 [workflow _13] start -DEBUG cwltool:workflow_job.py:777 [workflow _13] inputs { - "i1": 1 -} -INFO cwltool:workflow_job.py:613 [workflow _13] starting step subworkflow_2 -DEBUG cwltool:workflow_job.py:727 [step subworkflow_2] job input { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/i1": 1 -} -DEBUG cwltool:workflow_job.py:732 [step subworkflow_2] evaluated job input to { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/i1": 1 -} -INFO cwltool:workflow_job.py:75 [step subworkflow_2] start -DEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_2] produced output { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 2 -} -INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 1 completed success -INFO cwltool:workflow_job.py:75 [step subworkflow_2] start -DEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_2] produced output { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 3 -} -INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 2 completed success -INFO cwltool:workflow_job.py:75 [step subworkflow_2] start -DEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_2] produced output { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 4 -} -INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 3 completed success -INFO cwltool:workflow_job.py:75 [step subworkflow_2] start -DEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_2] produced output { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 5 -} -INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 4 completed success -INFO cwltool:workflow_job.py:75 [step subworkflow_2] start -DEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_2] produced output { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 6 -} -INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 5 completed success -INFO cwltool:workflow_job.py:75 [step subworkflow_2] start -DEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_2] produced output { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 7 -} -INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 6 completed success -INFO cwltool:workflow_job.py:75 [step subworkflow_2] start -DEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_2] produced output { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 8 -} -INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 7 completed success -INFO cwltool:workflow_job.py:75 [step subworkflow_2] start -DEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_2] produced output { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 9 -} -INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 8 completed success -INFO cwltool:workflow_job.py:75 [step subworkflow_2] start -DEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_2] produced output { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 10 -} -INFO cwltool:workflow_job.py:1005 [step subworkflow_2] Iteration 9 completed success -DEBUG cwltool:workflow_job.py:918 [step subworkflow_2] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9 -DEBUG cwltool:workflow_job.py:925 [step subworkflow_2] inputs was { - "i1": 10 -} -DEBUG cwltool:workflow_job.py:564 [step subworkflow_2] produced output { - "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop.cwl#subworkflow/o1": 10 -} -INFO cwltool:workflow_job.py:572 [step subworkflow_2] completed success -INFO cwltool:workflow_job.py:539 [workflow _13] completed success -DEBUG cwltool:workflow_job.py:541 [workflow _13] outputs { - "o1": 10 -} -DEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpyl41gacq -INFO cwltool:main.py:1366 Final process status is success@PPNdurationD?ðt.Ü?PNstartDAÙdõpÛ‡PNstopDAÙdõ²«ÞPN $report_typeN -TestReportPN -item_indexF¬PN worker_idNgw6PN testrun_uidN ca4970838f1b415dbaafd06f56809891PP@Qltool:job.py:419 [job count] completed success -DEBUG cwltool:job.py:422 [job count] outputs { - "line_count": { - "location": "file:///private/tmp/docker_tmp6x96v1_p/line_count", - "basename": "line_count", - "nameroot": "line_count", - "nameext": "", - "class": "File", - "checksum": "sha1$be56ebaa66bcaf15855bbdd6d1ec90e8bbfÚK«Úÿÿÿÿÿÿÿä data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable', 'location': ('tests/test_loop.py', 109, 'test_loop_single_variable'), 'keywords': {'test_loop_single_variable': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-lo finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable_no_iteration', 'location': ('tests/test_loop.py', 122, 'test_loop_single_variable_no_iteration'), 'keywords': {'test_loop_single_variable_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00020065800072188722, 'start': 1685951446.793686, 'stop': 1685951446.793887, '$report_type': 'TestReport', 'item_index': 429, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_loop_single_variable - location: ('tests/test_loop.py', 109, 'test_loop_single_variable') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_loop_single_variable_no_iteration - location: ('tests/test_loop.py', 122, 'test_loop_single_variable_no_iteration') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_environment', 'location': ('tests/test_mpi.py', 194, 'TestMpiRun.test_environment'), 'keywords': {'test_environment': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job mpi_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_env.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_env.cwl] /private/tmp/docker_tmp156vbda6$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 1 \\\n --no-fail \\\n env > /private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_env.cwl] outputs {\n "environment": {\n "location": "file:///private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "basename": "fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "nameroot": "fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$0088a72a33becb2278fc4741a6d88339fd6f2210",\n "size": 1098,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_env.cwl] Removing input staging directory /private/tmp/docker_tmphcj1vukp\nDEBUG cwltool:job.py:454 [job mpi_env.cwl] Removing temporary directory /private/tmp/docker_tmpg8c5bbwz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_environment0/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp156vbda6\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9825167569997575, 'start': 1685951446.030616, 'stop': 1685951447.013109, '$report_type': 'TestReport', 'item_index': 459, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::TestMpiRun::test_environment', 'location': ('tests/test_mpi.py', 194, 'TestMpiRun.test_environment'), 'keywords': {'test_environment': 1, 'TestMpiRun': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job mpi_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/mpi_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job mpi_env.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job mpi_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job mpi_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "env"\n }\n]\nDEBUG cwltool:job.py:215 [job mpi_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job mpi_env.cwl] /private/tmp/docker_tmp156vbda6$ /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/fake_mpi0/fake_mpirun \\\n --num \\\n 1 \\\n --no-fail \\\n env > /private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job mpi_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job mpi_env.cwl] outputs {\n "environment": {\n "location": "file:///private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "basename": "fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "nameroot": "fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$0088a72a33becb2278fc4741a6d88339fd6f2210",\n "size": 1098,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job mpi_env.cwl] Removing input staging directory /private/tmp/docker_tmphcj1vukp\nDEBUG cwltool:job.py:454 [job mpi_env.cwl] Removing temporary directory /private/tmp/docker_tmpg8c5bbwz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp156vbda6/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_environment0/fe621bbeafcb673f9cfa3a85b1c3ebcebdb865d8\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp156vbda6\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0016772190001574927, 'start': 1685951447.013999, 'stop': 1685951447.015678, '$report_type': 'TestReport', 'item_index': 459, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::TestMpiRun::test_environment - location: ('tests/test_mpi.py', 194, 'TestMpiRun.test_environment') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::test_env_passing - location: ('tests/test_mpi.py', 219, 'test_env_passing') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_env_passing', 'location': ('tests/test_mpi.py', 219, 'test_env_passing'), 'keywords': {'test_env_passing': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006188460001794738, 'start': 1685951447.017211, 'stop': 1685951447.0178308, '$report_type': 'TestReport', 'item_index': 460, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_env_passing', 'location': ('tests/test_mpi.py', 219, 'test_env_passing'), 'keywords': {'test_env_passing': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0007053230001474731, 'start': 1685951447.0186088, 'stop': 1685951447.019315, '$report_type': 'TestReport', 'item_index': 460, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_env_passing', 'location': ('tests/test_mpi.py', 219, 'test_env_passing'), 'keywords': {'test_env_passing': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.000304819000120915, 'start': 1685951447.019708, 'stop': 1685951447.020014, '$report_type': 'TestReport', 'item_index': 460, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::test_env_passing - location: ('tests/test_mpi.py', 219, 'test_env_passing') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::test_singularity - location: ('tests/test_mpi.py', 317, 'test_singularity') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]'), 'keywords': {'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:46]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl'")], 'duration': 0.894511448999765, 'start': 1685951446.509061, 'stop': 1685951447.403552, '$report_type': 'TestReport', 'item_index': 481, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]'), 'keywords': {'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:46]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/operation/operation-single.cwl'")], 'duration': 0.0004022650000479189, 'start': 1685951447.404211, 'stop': 1685951447.404615, '$report_type': 'TestReport', 'item_index': 481, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl] - location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/operation/operation-single.cwl-tests/wf/operation/expect_operation-single_packed.cwl]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl] - location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]'), 'keywords': {'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00043142699996678857, 'start': 1685951447.4058828, 'stop': 1685951447.406315, '$report_type': 'TestReport', 'item_index': 482, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]'), 'keywords': {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task2_12\nDEBUG cwltool:workflow_job.py:727 [step task2_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_12\nDEBUG cwltool:command_line_tool.py:988 [job task2_10] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_10] initial work dir {}\nINFO cwltool:job.py:266 [job task2_10] /private/tmp/docker_tmp2edpsbck$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2edpsbck,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwpqrjecs,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095045-366456.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_10] completed success\nDEBUG cwltool:job.py:422 [job task2_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2edpsbck/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_12] completed success\nDEBUG cwltool:job.py:446 [job task2_10] Removing input staging directory /private/tmp/docker_tmpparyqua4\nDEBUG cwltool:job.py:454 [job task2_10] Removing temporary directory /private/tmp/docker_tmpwpqrjecs\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task1_12\nDEBUG cwltool:workflow_job.py:727 [step task1_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_12\nDEBUG cwltool:command_line_tool.py:988 [job task1_10] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_10] initial work dir {}\nINFO cwltool:job.py:266 [job task1_10] /private/tmp/docker_tmpl6uhq9ur$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpl6uhq9ur,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp3v2v_ylx,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095046-398112.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_10] completed success\nDEBUG cwltool:job.py:422 [job task1_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpl6uhq9ur/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_12] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {}\nDEBUG cwltool:job.py:446 [job task1_10] Removing input staging directory /private/tmp/docker_tmp7cq588zt\nDEBUG cwltool:job.py:454 [job task1_10] Removing temporary directory /private/tmp/docker_tmp3v2v_ylx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmbshxay5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpl6uhq9ur\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2edpsbck\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 3.559965896999529, 'start': 1685951443.858878, 'stop': 1685951447.418756, '$report_type': 'TestReport', 'item_index': 278, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]'), 'keywords': {'test_cid_file_w_prefix[--debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _12] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _12] start\nDEBUG cwltool:workflow_job.py:777 [workflow _12] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task2_12\nDEBUG cwltool:workflow_job.py:727 [step task2_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_12\nDEBUG cwltool:command_line_tool.py:988 [job task2_10] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task2_10] initial work dir {}\nINFO cwltool:job.py:266 [job task2_10] /private/tmp/docker_tmp2edpsbck$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2edpsbck,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpwpqrjecs,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095045-366456.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_10] completed success\nDEBUG cwltool:job.py:422 [job task2_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2edpsbck/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_12] completed success\nDEBUG cwltool:job.py:446 [job task2_10] Removing input staging directory /private/tmp/docker_tmpparyqua4\nDEBUG cwltool:job.py:454 [job task2_10] Removing temporary directory /private/tmp/docker_tmpwpqrjecs\nINFO cwltool:workflow_job.py:613 [workflow _12] starting step task1_12\nDEBUG cwltool:workflow_job.py:727 [step task1_12] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_12] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_12] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_10] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_12\nDEBUG cwltool:command_line_tool.py:988 [job task1_10] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_10] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_10] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_10] initial work dir {}\nINFO cwltool:job.py:266 [job task1_10] /private/tmp/docker_tmpl6uhq9ur$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpl6uhq9ur,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp3v2v_ylx,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___debug0/pytestcid-20230605095046-398112.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:905 [job task1_10] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_10] completed success\nDEBUG cwltool:job.py:422 [job task1_10] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpl6uhq9ur/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_12] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_12] completed success\nINFO cwltool:workflow_job.py:539 [workflow _12] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _12] outputs {}\nDEBUG cwltool:job.py:446 [job task1_10] Removing input staging directory /private/tmp/docker_tmp7cq588zt\nDEBUG cwltool:job.py:454 [job task1_10] Removing temporary directory /private/tmp/docker_tmp3v2v_ylx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmbshxay5\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpl6uhq9ur\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2edpsbck\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000630780999927083, 'start': 1685951447.419929, 'stop': 1685951447.4205608, '$report_type': 'TestReport', 'item_index': 278, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--debug]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]'), 'keywords': {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0019516170004862943, 'start': 1685951447.422921, 'stop': 1685951447.424876, '$report_type': 'TestReport', 'item_index': 279, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters4-result4]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters4-result4]'), 'keywords': {'test_overrides[parameters4-result4]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters4-result4': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _14] start\n\x1b[1;30mINFO\x1b[0m [workflow _14] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmpnetcp5i3$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpnetcp5i3/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _14] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmpnetcp5i3$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpnetcp5i3/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello2\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpgmam1inb\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpno95obow\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnetcp5i3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptrv1sfqx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.733346445999814, 'start': 1685951446.697649, 'stop': 1685951447.430978, '$report_type': 'TestReport', 'item_index': 471, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters4-result4]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters4-result4]'), 'keywords': {'test_overrides[parameters4-result4]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters4-result4': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _14] start\n\x1b[1;30mINFO\x1b[0m [workflow _14] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmpnetcp5i3$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpnetcp5i3/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _14] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmpnetcp5i3$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpnetcp5i3/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello2\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "out": "zing hello2\\n"\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpgmam1inb\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpno95obow\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnetcp5i3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptrv1sfqx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005950549993940513, 'start': 1685951447.432105, 'stop': 1685951447.4327009, '$report_type': 'TestReport', 'item_index': 471, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides[parameters4-result4] - location: ('tests/test_override.py', 76, 'test_overrides[parameters4-result4]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides[parameters5-result5] - location: ('tests/test_override.py', 76, 'test_overrides[parameters5-result5]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters5-result5]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters5-result5]'), 'keywords': {'test_overrides[parameters5-result5]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters5-result5': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005286280002110288, 'start': 1685951447.4340851, 'stop': 1685951447.434614, '$report_type': 'TestReport', 'item_index': 472, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]'), 'keywords': {'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl'")], 'duration': 0.10997923700051615, 'start': 1685951447.406658, 'stop': 1685951447.5166368, '$report_type': 'TestReport', 'item_index': 482, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]'), 'keywords': {'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/trick_revsort.cwl'")], 'duration': 0.00029306200030987384, 'start': 1685951447.517217, 'stop': 1685951447.517511, '$report_type': 'TestReport', 'item_index': 482, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl] - location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/trick_revsort.cwl-tests/wf/expect_trick_packed.cwl]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl] - location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]'), 'keywords': {'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00043338799969205866, 'start': 1685951447.518337, 'stop': 1685951447.518772, '$report_type': 'TestReport', 'item_index': 483, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]'), 'keywords': {'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl'\ntests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\ntests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl'\nWARNING salad:ref_resolver.py:1130 tests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\nWARNING salad:ref_resolver.py:1130 tests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined")], 'duration': 0.02941035300045769, 'start': 1685951447.5191061, 'stop': 1685951447.548518, '$report_type': 'TestReport', 'item_index': 483, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]'), 'keywords': {'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl'\ntests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\ntests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwd-passthrough1.cwl'\nWARNING salad:ref_resolver.py:1130 tests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined\nWARNING salad:ref_resolver.py:1130 tests/wf/iwd-passthrough1.cwl:17:3: object id 'tests/wf/iwd-passthrough1.cwl#filelist' previously defined")], 'duration': 0.00037038899972685613, 'start': 1685951447.549118, 'stop': 1685951447.54949, '$report_type': 'TestReport', 'item_index': 483, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl] - location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/iwd-passthrough1.cwl-tests/wf/expect_iwd-passthrough1_packed.cwl]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl] - location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005589559996224125, 'start': 1685951447.550621, 'stop': 1685951447.551181, '$report_type': 'TestReport', 'item_index': 484, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable_no_iteration', 'location': ('tests/test_loop.py', 122, 'test_loop_single_variable_no_iteration'), 'keywords': {'test_loop_single_variable_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/single-var-loop-no-iteration.cwl:26:7: object id 'tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _14] start\n\x1b[1;30mINFO\x1b[0m [workflow _14] starting step subworkflow_3\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _14] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop-no-iteration.cwl:26:7: object id \'tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step subworkflow_3\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_3] loop condition $(inputs.i1 < 1) evaluated to False at iteration 0\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_3] inputs was {\n "i1": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_3] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "o1": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpypaeahap\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.970427149999523, 'start': 1685951446.7942111, 'stop': 1685951447.7646148, '$report_type': 'TestReport', 'item_index': 429, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_single_variable_no_iteration', 'location': ('tests/test_loop.py', 122, 'test_loop_single_variable_no_iteration'), 'keywords': {'test_loop_single_variable_no_iteration': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/single-var-loop-no-iteration.cwl:26:7: object id 'tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _14] start\n\x1b[1;30mINFO\x1b[0m [workflow _14] starting step subworkflow_3\n\x1b[1;30mINFO\x1b[0m [step subworkflow_3] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _14] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/single-var-loop-no-iteration.cwl:26:7: object id \'tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "i1": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step subworkflow_3\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/i1": 1\n}\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_3] loop condition $(inputs.i1 < 1) evaluated to False at iteration 0\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_3] inputs was {\n "i1": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/single-var-loop-no-iteration.cwl#subworkflow/o1": null\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_3] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "o1": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpypaeahap\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0003115270001217141, 'start': 1685951447.765162, 'stop': 1685951447.765474, '$report_type': 'TestReport', 'item_index': 429, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables', 'location': ('tests/test_loop.py', 135, 'test_loop_two_variables'), 'keywords': {'test_loop_two_variables': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002811579997796798, 'start': 1685951447.766572, 'stop': 1685951447.7668538, '$report_type': 'TestReport', 'item_index': 430, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_loop_single_variable_no_iteration - location: ('tests/test_loop.py', 122, 'test_loop_single_variable_no_iteration') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_loop_two_variables - location: ('tests/test_loop.py', 135, 'test_loop_two_variables') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_singularity', 'location': ('tests/test_mpi.py', 317, 'test_singularity'), 'keywords': {'test_singularity': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.7677750800003196, 'start': 1685951447.021031, 'stop': 1685951447.788788, '$report_type': 'TestReport', 'item_index': 461, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_singularity', 'location': ('tests/test_mpi.py', 317, 'test_singularity'), 'keywords': {'test_singularity': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.007320910999624175, 'start': 1685951447.789354, 'stop': 1685951447.7966762, '$report_type': 'TestReport', 'item_index': 461, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_singularity', 'location': ('tests/test_mpi.py', 317, 'test_singularity'), 'keywords': {'test_singularity': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.00023004299964668462, 'start': 1685951447.7974741, 'stop': 1685951447.797705, '$report_type': 'TestReport', 'item_index': 461, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::test_singularity - location: ('tests/test_mpi.py', 317, 'test_singularity') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_udocker', 'location': ('tests/test_mpi.py', 324, 'test_udocker'), 'keywords': {'test_udocker': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003294099997219746, 'start': 1685951447.7988281, 'stop': 1685951447.799159, '$report_type': 'TestReport', 'item_index': 462, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::test_udocker - location: ('tests/test_mpi.py', 324, 'test_udocker') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_udocker', 'location': ('tests/test_mpi.py', 324, 'test_udocker'), 'keywords': {'test_udocker': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.008525170999746479, 'start': 1685951447.799621, 'stop': 1685951447.808148, '$report_type': 'TestReport', 'item_index': 462, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_udocker', 'location': ('tests/test_mpi.py', 324, 'test_udocker'), 'keywords': {'test_udocker': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.0002947040002254653, 'start': 1685951447.808861, 'stop': 1685951447.8091571, '$report_type': 'TestReport', 'item_index': 462, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::test_udocker - location: ('tests/test_mpi.py', 324, 'test_udocker') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::test_docker_hint - location: ('tests/test_mpi.py', 331, 'test_docker_hint') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_hint', 'location': ('tests/test_mpi.py', 331, 'test_docker_hint'), 'keywords': {'test_docker_hint': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00025352200009365333, 'start': 1685951447.8103979, 'stop': 1685951447.810652, '$report_type': 'TestReport', 'item_index': 463, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_hint', 'location': ('tests/test_mpi.py', 331, 'test_docker_hint'), 'keywords': {'test_docker_hint': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint DockerRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPI has been required while Docker is hinted, discarding Docker hint(s)\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint DockerRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature\nWARNING cwltool:command_line_tool.py:453 MPI has been required while Docker is hinted, discarding Docker hint(s)')], 'duration': 0.007302015000277606, 'start': 1685951447.81097, 'stop': 1685951447.818273, '$report_type': 'TestReport', 'item_index': 463, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_hint', 'location': ('tests/test_mpi.py', 331, 'test_docker_hint'), 'keywords': {'test_docker_hint': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint DockerRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPI has been required while Docker is hinted, discarding Docker hint(s)\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint DockerRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature\nWARNING cwltool:command_line_tool.py:453 MPI has been required while Docker is hinted, discarding Docker hint(s)')], 'duration': 0.0002557699999670149, 'start': 1685951447.8188071, 'stop': 1685951447.819063, '$report_type': 'TestReport', 'item_index': 463, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::test_docker_hint - location: ('tests/test_mpi.py', 331, 'test_docker_hint') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::test_docker_required - location: ('tests/test_mpi.py', 339, 'test_docker_required') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_required', 'location': ('tests/test_mpi.py', 339, 'test_docker_required'), 'keywords': {'test_docker_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003120929995930055, 'start': 1685951447.820271, 'stop': 1685951447.8205838, '$report_type': 'TestReport', 'item_index': 464, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_required', 'location': ('tests/test_mpi.py', 339, 'test_docker_required'), 'keywords': {'test_docker_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint http://commonwl.org/cwltool#MPIRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mDocker has been required while MPI is hinted, discarding MPI hint(s)\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint http://commonwl.org/cwltool#MPIRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature\nWARNING cwltool:command_line_tool.py:460 Docker has been required while MPI is hinted, discarding MPI hint(s)')], 'duration': 0.008689338999829488, 'start': 1685951447.821028, 'stop': 1685951447.829718, '$report_type': 'TestReport', 'item_index': 464, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_required', 'location': ('tests/test_mpi.py', 339, 'test_docker_required'), 'keywords': {'test_docker_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint http://commonwl.org/cwltool#MPIRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mDocker has been required while MPI is hinted, discarding MPI hint(s)\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint http://commonwl.org/cwltool#MPIRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature\nWARNING cwltool:command_line_tool.py:460 Docker has been required while MPI is hinted, discarding MPI hint(s)')], 'duration': 0.00021788699996250216, 'start': 1685951447.830179, 'stop': 1685951447.8303978, '$report_type': 'TestReport', 'item_index': 464, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_required', 'location': ('tests/test_mpi.py', 347, 'test_docker_mpi_both_required'), 'keywords': {'test_docker_mpi_both_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00027876399963133736, 'start': 1685951447.831475, 'stop': 1685951447.831756, '$report_type': 'TestReport', 'item_index': 465, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::test_docker_required - location: ('tests/test_mpi.py', 339, 'test_docker_required') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::test_docker_mpi_both_required - location: ('tests/test_mpi.py', 347, 'test_docker_mpi_both_required') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_required', 'location': ('tests/test_mpi.py', 347, 'test_docker_mpi_both_required'), 'keywords': {'test_docker_mpi_both_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', " \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\nreceived command runtests {'indices': [513, 514, 515, 516, 517, 518]}"), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.008565494999857037, 'start': 1685951447.832157, 'stop': 1685951447.840724, '$report_type': 'TestReport', 'item_index': 465, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_required', 'location': ('tests/test_mpi.py', 347, 'test_docker_mpi_both_required'), 'keywords': {'test_docker_mpi_both_required': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', " \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\nreceived command runtests {'indices': [513, 514, 515, 516, 517, 518]}"), ('Captured log call', 'WARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature'), ('Captured stderr teardown', '\n')], 'duration': 0.0002890880004997598, 'start': 1685951447.84132, 'stop': 1685951447.84161, '$report_type': 'TestReport', 'item_index': 465, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::test_docker_mpi_both_required - location: ('tests/test_mpi.py', 347, 'test_docker_mpi_both_required') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_mpi.py::test_docker_mpi_both_hinted - location: ('tests/test_mpi.py', 355, 'test_docker_mpi_both_hinted') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_hinted', 'location': ('tests/test_mpi.py', 355, 'test_docker_mpi_both_hinted'), 'keywords': {'test_docker_mpi_both_hinted': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003151740002067527, 'start': 1685951447.842783, 'stop': 1685951447.8430998, '$report_type': 'TestReport', 'item_index': 466, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_hinted', 'location': ('tests/test_mpi.py', 355, 'test_docker_mpi_both_hinted'), 'keywords': {'test_docker_mpi_both_hinted': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint http://commonwl.org/cwltool#MPIRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint DockerRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint http://commonwl.org/cwltool#MPIRequirement\nINFO cwltool:process.py:1070 Unknown hint DockerRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.06096013200021844, 'start': 1685951447.843498, 'stop': 1685951447.904458, '$report_type': 'TestReport', 'item_index': 466, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_mpi.py::test_docker_mpi_both_hinted', 'location': ('tests/test_mpi.py', 355, 'test_docker_mpi_both_hinted'), 'keywords': {'test_docker_mpi_both_hinted': 1, 'test_mpi.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint http://commonwl.org/cwltool#MPIRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Unknown hint DockerRequirement\n\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mMPIRequirement with containers is a beta feature\x1b[0m\n'), ('Captured log call', 'INFO cwltool:process.py:1070 Unknown hint http://commonwl.org/cwltool#MPIRequirement\nINFO cwltool:process.py:1070 Unknown hint DockerRequirement\nWARNING cwltool:command_line_tool.py:441 MPIRequirement with containers is a beta feature')], 'duration': 0.00019882299966411665, 'start': 1685951447.904893, 'stop': 1685951447.9050932, '$report_type': 'TestReport', 'item_index': 466, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_mpi.py::test_docker_mpi_both_hinted - location: ('tests/test_mpi.py', 355, 'test_docker_mpi_both_hinted') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides[parameters0-result0] - location: ('tests/test_override.py', 76, 'test_overrides[parameters0-result0]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters0-result0]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters0-result0]'), 'keywords': {'test_overrides[parameters0-result0]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-result0': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009969010006898316, 'start': 1685951447.906661, 'stop': 1685951447.907661, '$report_type': 'TestReport', 'item_index': 467, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters5-result5]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters5-result5]'), 'keywords': {'test_overrides[parameters5-result5]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters5-result5': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpj04h1f3l$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpj04h1f3l/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpj04h1f3l$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpj04h1f3l/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "out": "zing hello5\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello5\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": "zing hello5\\n"\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpvw9dygow\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpe804kt2a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvimgwujy\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj04h1f3l\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7897590640004637, 'start': 1685951447.434944, 'stop': 1685951448.224685, '$report_type': 'TestReport', 'item_index': 472, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters5-result5]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters5-result5]'), 'keywords': {'test_overrides[parameters5-result5]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters5-result5': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpj04h1f3l$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpj04h1f3l/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpj04h1f3l$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpj04h1f3l/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "out": "zing hello5\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello5\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": "zing hello5\\n"\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpvw9dygow\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpe804kt2a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvimgwujy\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj04h1f3l\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007478079996872111, 'start': 1685951448.2257411, 'stop': 1685951448.22649, '$report_type': 'TestReport', 'item_index': 472, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides[parameters5-result5] - location: ('tests/test_override.py', 76, 'test_overrides[parameters5-result5]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides[parameters6-result6] - location: ('tests/test_override.py', 76, 'test_overrides[parameters6-result6]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters6-result6]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters6-result6]'), 'keywords': {'test_overrides[parameters6-result6]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters6-result6': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009183920001305523, 'start': 1685951448.228301, 'stop': 1685951448.2292202, '$report_type': 'TestReport', 'item_index': 473, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters0-result0]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters0-result0]'), 'keywords': {'test_overrides[parameters0-result0]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-result0': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_2] /private/tmp/docker_tmpfp0t3l3u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpfp0t3l3u/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_2] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_2] /private/tmp/docker_tmpfp0t3l3u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpfp0t3l3u/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_2] outputs {\n "out": "zing hello1\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_2] Removing input staging directory /private/tmp/docker_tmpeqs91hzx\nDEBUG cwltool:job.py:454 [job echo.cwl_2] Removing temporary directory /private/tmp/docker_tmp40o02aoz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfp0t3l3u\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.730464029000359, 'start': 1685951447.908118, 'stop': 1685951448.638567, '$report_type': 'TestReport', 'item_index': 467, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters0-result0]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters0-result0]'), 'keywords': {'test_overrides[parameters0-result0]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-result0': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl'\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_2] /private/tmp/docker_tmpfp0t3l3u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpfp0t3l3u/out.txt\n\x1b[1;30mINFO\x1b[0m [job echo.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl_2] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl_2] /private/tmp/docker_tmpfp0t3l3u$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpfp0t3l3u/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl_2] outputs {\n "out": "zing hello1\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl_2] Removing input staging directory /private/tmp/docker_tmpeqs91hzx\nDEBUG cwltool:job.py:454 [job echo.cwl_2] Removing temporary directory /private/tmp/docker_tmp40o02aoz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfp0t3l3u\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.001413670000147249, 'start': 1685951448.6403031, 'stop': 1685951448.641719, '$report_type': 'TestReport', 'item_index': 467, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides[parameters0-result0] - location: ('tests/test_override.py', 76, 'test_overrides[parameters0-result0]') - 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slashes-file_dir0-expected0': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00043503899996721884, 'start': 1685951448.645837, 'stop': 1685951448.6462731, '$report_type': 'TestReport', 'item_index': 513, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]'), 'keywords': {'test_normalizeFilesDirs[strip trailing slashes-file_dir0-expected0]': 1, 'parametrize': 1, 'pytestmark': 1, 'strip trailing slashes-file_dir0-expected0': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0005063790003987378, 'start': 1685951448.646919, 'stop': 1685951448.647427, '$report_type': 'TestReport', 'item_index': 513, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: 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'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008652080005049356, 'start': 1685951448.649068, 'stop': 1685951448.649935, '$report_type': 'TestReport', 'item_index': 514, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file-file_dir1-expected1]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file-file_dir1-expected1]'), 'keywords': {'test_normalizeFilesDirs[file-file_dir1-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, 'file-file_dir1-expected1': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004152450001129182, 'start': 1685951448.650466, 'stop': 1685951448.650882, '$report_type': 'TestReport', 'item_index': 514, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file-file_dir1-expected1]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file-file_dir1-expected1]'), 'keywords': {'test_normalizeFilesDirs[file-file_dir1-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, 'file-file_dir1-expected1': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00046641399967484176, 'start': 1685951448.651627, 'stop': 1685951448.652096, '$report_type': 'TestReport', 'item_index': 514, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pathmapper.py::test_normalizeFilesDirs[file-file_dir1-expected1] - location: 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'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0008206479997170391, 'start': 1685951448.6534479, 'stop': 1685951448.65427, '$report_type': 'TestReport', 'item_index': 515, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file with local uri-file_dir2-expected2]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with local uri-file_dir2-expected2]'), 'keywords': {'test_normalizeFilesDirs[file with local uri-file_dir2-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, 'file with local uri-file_dir2-expected2': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005807630004710518, 'start': 1685951448.654985, 'stop': 1685951448.655568, '$report_type': 'TestReport', 'item_index': 515, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file with local uri-file_dir2-expected2]', 'location': 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url-file_dir3-expected3': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001273665000553592, 'start': 1685951448.658586, 'stop': 1685951448.659861, '$report_type': 'TestReport', 'item_index': 516, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file with http url-file_dir3-expected3]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file with http 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'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004950350003127824, 'start': 1685951448.671987, 'stop': 1685951448.672485, '$report_type': 'TestReport', 'item_index': 519, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[.foo-expected2]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[.foo-expected2]'), 'keywords': 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'start': 1685951448.676179, 'stop': 1685951448.676575, '$report_type': 'TestReport', 'item_index': 520, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_basename_field_generation[foo.-expected3]', 'location': ('tests/test_pathmapper.py', 82, 'test_basename_field_generation[foo.-expected3]'), 'keywords': {'test_basename_field_generation[foo.-expected3]': 1, 'parametrize': 1, 'pytestmark': 1, 'foo.-expected3': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': 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[hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_procgenerator.py::test_missing_enable_ext', 'location': ('tests/test_procgenerator.py', 11, 'test_missing_enable_ext'), 'keywords': {'test_missing_enable_ext': 1, 'test_procgenerator.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw5] received command runtests {'indices': [525, 526, 527, 528, 529]}\n")], 'duration': 0.0021776809999209945, 'start': 1685951448.683458, 'stop': 1685951448.6856372, '$report_type': 'TestReport', 'item_index': 522, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables', 'location': ('tests/test_loop.py', 135, 'test_loop_two_variables'), 'keywords': {'test_loop_two_variables': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/two-vars-loop.cwl:28:7: object id 'tests/loop/two-vars-loop.cwl#subworkflow/i1' previously defined\ntests/loop/two-vars-loop.cwl:29:7: object id 'tests/loop/two-vars-loop.cwl#subworkflow/i2' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step subworkflow_4\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop.cwl:28:7: object id \'tests/loop/two-vars-loop.cwl#subworkflow/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop.cwl:29:7: object id \'tests/loop/two-vars-loop.cwl#subworkflow/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step subworkflow_4\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 6,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 7,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 8,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 9,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 10,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_4] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_4] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 10,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpb71y25y0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0642764849999367, 'start': 1685951447.7672498, 'stop': 1685951448.831501, '$report_type': 'TestReport', 'item_index': 430, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables', 'location': ('tests/test_loop.py', 135, 'test_loop_two_variables'), 'keywords': {'test_loop_two_variables': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/two-vars-loop.cwl:28:7: object id 'tests/loop/two-vars-loop.cwl#subworkflow/i1' previously defined\ntests/loop/two-vars-loop.cwl:29:7: object id 'tests/loop/two-vars-loop.cwl#subworkflow/i2' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step subworkflow_4\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop.cwl:28:7: object id \'tests/loop/two-vars-loop.cwl#subworkflow/i1\' previously defined\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop.cwl:29:7: object id \'tests/loop/two-vars-loop.cwl#subworkflow/i2\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step subworkflow_4\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 2,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 3,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 4,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 5,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 6,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 7,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 8,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 9,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_4] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 10,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_4] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_4] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_4] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o1": 10,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop.cwl#subworkflow/o2": 1\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpb71y25y0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00027263499941909686, 'start': 1685951448.8321788, 'stop': 1685951448.832453, '$report_type': 'TestReport', 'item_index': 430, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_loop_two_variables - location: ('tests/test_loop.py', 135, 'test_loop_two_variables') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_loop.py::test_loop_two_variables_single_backpropagation - location: ('tests/test_loop.py', 148, 'test_loop_two_variables_single_backpropagation') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables_single_backpropagation', 'location': ('tests/test_loop.py', 148, 'test_loop_two_variables_single_backpropagation'), 'keywords': {'test_loop_two_variables_single_backpropagation': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00021312199987733038, 'start': 1685951448.8346372, 'stop': 1685951448.834851, '$report_type': 'TestReport', 'item_index': 431, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters6-result6]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters6-result6]'), 'keywords': {'test_overrides[parameters6-result6]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters6-result6': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_3] /private/tmp/docker_tmpom9d8ntn$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpom9d8ntn/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpom9d8ntn$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpom9d8ntn/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": "zing hello6\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello6\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "out": "zing hello6\\n"\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfoeamufx\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmpt43592ho\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpom9d8ntn\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpacyeypq2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9073105670004225, 'start': 1685951448.2299478, 'stop': 1685951449.137239, '$report_type': 'TestReport', 'item_index': 473, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters6-result6]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters6-result6]'), 'keywords': {'test_overrides[parameters6-result6]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters6-result6': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_3] /private/tmp/docker_tmpom9d8ntn$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpom9d8ntn/out.txt\n\x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "m1": "zing"\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/m1": "zing"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/echo.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "m1": "zing"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.m1)"\n },\n {\n "shellQuote": false,\n "valueFrom": "$MESSAGE",\n "position": [\n 0,\n 2\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpom9d8ntn$ /bin/sh \\\n -c \\\n echo zing $MESSAGE > /private/tmp/docker_tmpom9d8ntn/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": "zing hello6\\n"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/override/echo-wf.cwl#step1/out": "zing hello6\\n"\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "out": "zing hello6\\n"\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfoeamufx\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmpt43592ho\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpom9d8ntn\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpacyeypq2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006992500002525048, 'start': 1685951449.138462, 'stop': 1685951449.1391628, '$report_type': 'TestReport', 'item_index': 473, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides[parameters6-result6] - location: ('tests/test_override.py', 76, 'test_overrides[parameters6-result6]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides[parameters7-result7] - location: ('tests/test_override.py', 76, 'test_overrides[parameters7-result7]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters7-result7]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters7-result7]'), 'keywords': {'test_overrides[parameters7-result7]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters7-result7': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0009293820003222208, 'start': 1685951449.141689, 'stop': 1685951449.1426198, '$report_type': 'TestReport', 'item_index': 474, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]'), 'keywords': {'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:45]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[1;30mINFO\x1b[0m [workflow _3] start\n\x1b[1;30mINFO\x1b[0m [workflow _3] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmp26s71h5c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp26s71h5c,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpol7xhy3g,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp_0898t8u/20230605095045-906739.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt > /private/tmp/docker_tmp26s71h5c/output\n\x1b[1;30mINFO\x1b[0m [job step1] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _3] starting step step2\n\x1b[1;30mINFO\x1b[0m [step step2] start\n\x1b[1;30mINFO\x1b[0m [step step2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _3] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] initialized from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] starting step step1_2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#wc-tool.cwl as part of step step1_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] initial work dir {}\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1_2] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmp77etqg31$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp77etqg31,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp69rybhp1,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp7z_ke77g/20230605095048-545487.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt > /private/tmp/docker_tmp77etqg31/output\n\x1b[1;30mINFO\x1b[0m [job step1_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] Removing input staging directory /private/tmp/docker_tmpt4xj39bu\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] Removing temporary directory /private/tmp/docker_tmp69rybhp1\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] starting step step2_2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_2] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/output": 16\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] outputs {\n "count_output": 16\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpfdsc75o7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp77etqg31\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp26s71h5c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp26s71h5c,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpol7xhy3g,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp_0898t8u/20230605095045-906739.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt > /private/tmp/docker_tmp26s71h5c/output\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpl05vyv1q\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpol7xhy3g\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step2\nDEBUG cwltool:workflow_job.py:727 [step step2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2] start\nDEBUG cwltool:workflow_job.py:564 [step step2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppuyriqxl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp26s71h5c\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\'\nDEBUG cwltool:workflow_job.py:498 [workflow _4] initialized from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main\nINFO cwltool:workflow_job.py:765 [workflow _4] start\nDEBUG cwltool:workflow_job.py:777 [workflow _4] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _4] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#wc-tool.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1_2] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmp77etqg31$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp77etqg31,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp69rybhp1,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp7z_ke77g/20230605095048-545487.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt > /private/tmp/docker_tmp77etqg31/output\nINFO cwltool:job.py:905 [job step1_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpt4xj39bu\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmp69rybhp1\nINFO cwltool:workflow_job.py:613 [workflow _4] starting step step2_2\nDEBUG cwltool:workflow_job.py:727 [step step2_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_2] start\nDEBUG cwltool:workflow_job.py:564 [step step2_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _4] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfdsc75o7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp77etqg31\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 4.536852426000223, 'start': 1685951445.0456069, 'stop': 1685951449.582348, '$report_type': 'TestReport', 'item_index': 492, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]'), 'keywords': {'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:45]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[1;30mINFO\x1b[0m [workflow _3] start\n\x1b[1;30mINFO\x1b[0m [workflow _3] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmp26s71h5c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp26s71h5c,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpol7xhy3g,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp_0898t8u/20230605095045-906739.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt > /private/tmp/docker_tmp26s71h5c/output\n\x1b[1;30mINFO\x1b[0m [job step1] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _3] starting step step2\n\x1b[1;30mINFO\x1b[0m [step step2] start\n\x1b[1;30mINFO\x1b[0m [step step2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _3] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] initialized from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] starting step step1_2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#wc-tool.cwl as part of step step1_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] initial work dir {}\x1b[0m\n\x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1_2] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmp77etqg31$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp77etqg31,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp69rybhp1,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp7z_ke77g/20230605095048-545487.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt > /private/tmp/docker_tmp77etqg31/output\n\x1b[1;30mINFO\x1b[0m [job step1_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] Removing input staging directory /private/tmp/docker_tmpt4xj39bu\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_2] Removing temporary directory /private/tmp/docker_tmp69rybhp1\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _4] starting step step2_2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_2] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/output": 16\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _4] outputs {\n "count_output": 16\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpfdsc75o7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp77etqg31\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp26s71h5c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp26s71h5c,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpol7xhy3g,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp_0898t8u/20230605095045-906739.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stgead0f8a8-2c75-4513-bdb6-7c8eb762dc11/whale.txt > /private/tmp/docker_tmp26s71h5c/output\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpl05vyv1q\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpol7xhy3g\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step2\nDEBUG cwltool:workflow_job.py:727 [step step2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///private/tmp/docker_tmp26s71h5c/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2] start\nDEBUG cwltool:workflow_job.py:564 [step step2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppuyriqxl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp26s71h5c\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf\'\nDEBUG cwltool:workflow_job.py:498 [workflow _4] initialized from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main\nINFO cwltool:workflow_job.py:765 [workflow _4] start\nDEBUG cwltool:workflow_job.py:777 [workflow _4] inputs {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _4] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#wc-tool.cwl as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1_2] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmp77etqg31$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp77etqg31,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp69rybhp1,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp7z_ke77g/20230605095048-545487.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stga2390f67-38f8-49eb-94d5-5b9275a77c68/whale.txt > /private/tmp/docker_tmp77etqg31/output\nINFO cwltool:job.py:905 [job step1_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step1/output": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpt4xj39bu\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmp69rybhp1\nINFO cwltool:workflow_job.py:613 [workflow _4] starting step step2_2\nDEBUG cwltool:workflow_job.py:727 [step step2_2] job input {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_2] evaluated job input to {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/file1": {\n "location": "file:///private/tmp/docker_tmp77etqg31/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_2] start\nDEBUG cwltool:workflow_job.py:564 [step step2_2] produced output {\n "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7m_6x7hf#main/step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _4] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _4] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfdsc75o7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp77etqg31\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0011825430001408677, 'start': 1685951449.584609, 'stop': 1685951449.585794, '$report_type': 'TestReport', 'item_index': 492, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False] - location: ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/count-lines1-wf.cwl-tests/wf/wc-job.json-False]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True] - location: ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]'), 'keywords': {'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/formattest.cwl-tests/wf/formattest-job.json-True': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.002233817000160343, 'start': 1685951449.588507, 'stop': 1685951449.590742, '$report_type': 'TestReport', 'item_index': 493, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables_single_backpropagation', 'location': ('tests/test_loop.py', 148, 'test_loop_two_variables_single_backpropagation'), 'keywords': {'test_loop_two_variables_single_backpropagation': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/two-vars-loop-2.cwl:27:7: object id 'tests/loop/two-vars-loop-2.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step subworkflow_5\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop-2.cwl:27:7: object id \'tests/loop/two-vars-loop-2.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step subworkflow_5\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_5] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_5] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5pf69jm7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0921014760006074, 'start': 1685951448.835296, 'stop': 1685951449.927371, '$report_type': 'TestReport', 'item_index': 431, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_loop.py::test_loop_two_variables_single_backpropagation', 'location': ('tests/test_loop.py', 148, 'test_loop_two_variables_single_backpropagation'), 'keywords': {'test_loop_two_variables_single_backpropagation': 1, 'test_loop.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl'\nURI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\ntests/loop/two-vars-loop-2.cwl:27:7: object id 'tests/loop/two-vars-loop-2.cwl#subworkflow/i1' previously defined\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step subworkflow_5\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 1 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 2 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 3 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 4 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 5 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 6 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 7 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 8 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] start\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] Iteration 9 completed success\n\x1b[1;30mINFO\x1b[0m [step subworkflow_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\'\nWARNING salad:ref_resolver.py:240 URI prefix \'cwltool\' of \'cwltool:loop\' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1130 tests/loop/two-vars-loop-2.cwl:27:7: object id \'tests/loop/two-vars-loop-2.cwl#subworkflow/i1\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "i1": 1,\n "i2": 1\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step subworkflow_5\nDEBUG cwltool:workflow_job.py:727 [step subworkflow_5] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i2": 1\n}\nDEBUG cwltool:workflow_job.py:732 [step subworkflow_5] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i1": 1,\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/i2": 1\n}\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 1 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 2\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 1 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 2 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 3\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 2 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 3 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 4\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 3 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 4 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 5\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 4 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 5 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 6\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 5 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 6 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 7\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 6 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 7 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 8\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 7 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 8 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 9\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 8 completed success\nINFO cwltool:workflow_job.py:75 [step subworkflow_5] start\nDEBUG cwltool:workflow_job.py:987 Iteration 9 of [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:1005 [step subworkflow_5] Iteration 9 completed success\nDEBUG cwltool:workflow_job.py:918 [step subworkflow_5] loop condition $(inputs.i1 < 10) evaluated to False at iteration 9\nDEBUG cwltool:workflow_job.py:925 [step subworkflow_5] inputs was {\n "i1": 10,\n "i2": 1\n}\nDEBUG cwltool:workflow_job.py:564 [step subworkflow_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/loop/two-vars-loop-2.cwl#subworkflow/o1": 10\n}\nINFO cwltool:workflow_job.py:572 [step subworkflow_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "o1": 10\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5pf69jm7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00025226599973393604, 'start': 1685951449.9279418, 'stop': 1685951449.928195, '$report_type': 'TestReport', 'item_index': 431, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_loop.py::test_loop_two_variables_single_backpropagation - location: ('tests/test_loop.py', 148, 'test_loop_two_variables_single_backpropagation') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_secondary_files_output - location: ('tests/test_provenance.py', 160, 'test_secondary_files_output') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_output', 'location': ('tests/test_provenance.py', 160, 'test_secondary_files_output'), 'keywords': {'test_secondary_files_output': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0010687859994504834, 'start': 1685951449.9292428, 'stop': 1685951449.930312, '$report_type': 'TestReport', 'item_index': 530, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters7-result7]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters7-result7]'), 'keywords': {'test_overrides[parameters7-result7]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters7-result7': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\'\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.cwl] /private/tmp/docker_tmp_n9dj204$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmp_n9dj204/cwl.output.json\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool_v1.1.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool_v1.1.cwl] {\n "in": "hello test env",\n "https://w3id.org/cwl/cwl#requirements": [\n {\n "class": "EnvVarRequirement",\n "envDef": [\n {\n "envName": "TEST_ENV",\n "envValue": "$(inputs.in)"\n }\n ]\n }\n ]\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool_v1.1.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool_v1.1.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo {\\\\\\"value\\\\\\": \\\\\\"$TEST_ENV\\\\\\"}"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool_v1.1.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool_v1.1.cwl] /private/tmp/docker_tmp_n9dj204$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmp_n9dj204/cwl.output.json\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:1222 Raw output from /private/tmp/docker_tmp_n9dj204/cwl.output.json: {\n "value": "hello test env"\n}\nINFO cwltool:job.py:419 [job env-tool_v1.1.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool_v1.1.cwl] outputs {\n "value": "hello test env"\n}\nDEBUG cwltool:job.py:446 [job env-tool_v1.1.cwl] Removing input staging directory /private/tmp/docker_tmpgx1egott\nDEBUG cwltool:job.py:454 [job env-tool_v1.1.cwl] Removing temporary directory /private/tmp/docker_tmpp_di2gaz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_n9dj204\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.8655887819995769, 'start': 1685951449.143234, 'stop': 1685951450.008804, '$report_type': 'TestReport', 'item_index': 474, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters7-result7]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters7-result7]'), 'keywords': {'test_overrides[parameters7-result7]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters7-result7': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\'\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.cwl] /private/tmp/docker_tmp_n9dj204$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmp_n9dj204/cwl.output.json\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool_v1.1.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool_v1.1.cwl] {\n "in": "hello test env",\n "https://w3id.org/cwl/cwl#requirements": [\n {\n "class": "EnvVarRequirement",\n "envDef": [\n {\n "envName": "TEST_ENV",\n "envValue": "$(inputs.in)"\n }\n ]\n }\n ]\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool_v1.1.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool_v1.1.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo {\\\\\\"value\\\\\\": \\\\\\"$TEST_ENV\\\\\\"}"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool_v1.1.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool_v1.1.cwl] /private/tmp/docker_tmp_n9dj204$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmp_n9dj204/cwl.output.json\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:1222 Raw output from /private/tmp/docker_tmp_n9dj204/cwl.output.json: {\n "value": "hello test env"\n}\nINFO cwltool:job.py:419 [job env-tool_v1.1.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool_v1.1.cwl] outputs {\n "value": "hello test env"\n}\nDEBUG cwltool:job.py:446 [job env-tool_v1.1.cwl] Removing input staging directory /private/tmp/docker_tmpgx1egott\nDEBUG cwltool:job.py:454 [job env-tool_v1.1.cwl] Removing temporary directory /private/tmp/docker_tmpp_di2gaz\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_n9dj204\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008864490000632941, 'start': 1685951450.01002, 'stop': 1685951450.0109088, '$report_type': 'TestReport', 'item_index': 474, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides[parameters7-result7] - location: ('tests/test_override.py', 76, 'test_overrides[parameters7-result7]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides[parameters8-result8] - location: ('tests/test_override.py', 76, 'test_overrides[parameters8-result8]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters8-result8]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters8-result8]'), 'keywords': {'test_overrides[parameters8-result8]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters8-result8': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007296699996004463, 'start': 1685951450.0127401, 'stop': 1685951450.013471, '$report_type': 'TestReport', 'item_index': 475, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]'), 'keywords': {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task1_13\nDEBUG cwltool:workflow_job.py:727 [step task1_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_13\nDEBUG cwltool:command_line_tool.py:988 [job task1_11] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_11), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task2_13\nDEBUG cwltool:workflow_job.py:727 [step task2_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_13\nDEBUG cwltool:command_line_tool.py:988 [job task2_11] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_11] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_11), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_11] initial work dir {}\nINFO cwltool:job.py:266 [job task1_11] /private/tmp/docker_tmp4m9l14lt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp4m9l14lt,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpexenol_6,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-096004.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:266 [job task2_11] /private/tmp/docker_tmpq2su4gxh$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpq2su4gxh,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmplu6a4tzl,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-110322.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task1_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_11] completed success\nDEBUG cwltool:job.py:422 [job task1_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp4m9l14lt/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_13] completed success\nDEBUG cwltool:job.py:446 [job task1_11] Removing input staging directory /private/tmp/docker_tmpqp3usw7p\nDEBUG cwltool:job.py:454 [job task1_11] Removing temporary directory /private/tmp/docker_tmpexenol_6\nINFO cwltool:job.py:905 [job task2_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_11] completed success\nDEBUG cwltool:job.py:422 [job task2_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpq2su4gxh/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_13] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {}\nDEBUG cwltool:job.py:446 [job task2_11] Removing input staging directory /private/tmp/docker_tmp7r_dkuxt\nDEBUG cwltool:job.py:454 [job task2_11] Removing temporary directory /private/tmp/docker_tmplu6a4tzl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp4m9l14lt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzpg9e3kx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpq2su4gxh\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.7110078599998815, 'start': 1685951447.425432, 'stop': 1685951450.136374, '$report_type': 'TestReport', 'item_index': 279, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug]', 'location': ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]'), 'keywords': {'test_cid_file_w_prefix[--parallel --debug]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '--parallel --debug': 1, 'test_examples.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _13] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _13] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task1_13\nDEBUG cwltool:workflow_job.py:727 [step task1_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nDEBUG cwltool:workflow_job.py:732 [step task1_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task1/message": "one"\n}\nINFO cwltool:workflow_job.py:75 [step task1_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task1_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task1_13\nDEBUG cwltool:command_line_tool.py:988 [job task1_11] {\n "message": "one"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task1_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task1_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "one"\n }\n]\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:765 [workflow _13] start\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task1_11), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:613 [workflow _13] starting step task2_13\nDEBUG cwltool:workflow_job.py:727 [step task2_13] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2_13] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2_13] start\nDEBUG cwltool:command_line_tool.py:982 [job task2_11] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2_13\nDEBUG cwltool:command_line_tool.py:988 [job task2_11] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2_11] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2_11] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nDEBUG cwltool:job.py:215 [job task1_11] initial work dir {}\nDEBUG cwltool:executors.py:309 job: CommandLineJob(task2_11), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job task2_11] initial work dir {}\nINFO cwltool:job.py:266 [job task1_11] /private/tmp/docker_tmp4m9l14lt$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp4m9l14lt,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmpexenol_6,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-096004.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n one\nINFO cwltool:job.py:266 [job task2_11] /private/tmp/docker_tmpq2su4gxh$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpq2su4gxh,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmplu6a4tzl,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_cid_file_w_prefix___paral1/pytestcid-20230605095049-110322.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task1_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task1_11] completed success\nDEBUG cwltool:job.py:422 [job task1_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp4m9l14lt/one",\n "basename": "one",\n "nameroot": "one",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task1_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task1_13] completed success\nDEBUG cwltool:job.py:446 [job task1_11] Removing input staging directory /private/tmp/docker_tmpqp3usw7p\nDEBUG cwltool:job.py:454 [job task1_11] Removing temporary directory /private/tmp/docker_tmpexenol_6\nINFO cwltool:job.py:905 [job task2_11] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2_11] completed success\nDEBUG cwltool:job.py:422 [job task2_11] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpq2su4gxh/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2_13] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2_13] completed success\nINFO cwltool:workflow_job.py:539 [workflow _13] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _13] outputs {}\nDEBUG cwltool:job.py:446 [job task2_11] Removing input staging directory /private/tmp/docker_tmp7r_dkuxt\nDEBUG cwltool:job.py:454 [job task2_11] Removing temporary directory /private/tmp/docker_tmplu6a4tzl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp4m9l14lt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzpg9e3kx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpq2su4gxh\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006579000000783708, 'start': 1685951450.137392, 'stop': 1685951450.138051, '$report_type': 'TestReport', 'item_index': 279, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_examples.py::test_cid_file_w_prefix[--parallel --debug] - location: ('tests/test_examples.py', 1137, 'test_cid_file_w_prefix[--parallel --debug]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\uadf8\\ub798\\ud504]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]'), 'keywords': {'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0021395619996837922, 'start': 1685951450.139597, 'stop': 1685951450.141738, '$report_type': 'TestReport', 'item_index': 505, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_require_prefix_networkaccess', 'location': ('tests/test_ext.py', 234, 'test_require_prefix_networkaccess'), 'keywords': {'test_require_prefix_networkaccess': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', '[worker-gw2] received command runtests {\'indices\': [497, 498, 499, 500, 501, 502, 503, 504]}\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] /private/tmp/docker_tmp75dfw90k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp75dfw90k,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp2jf3vw_z,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp1vsmbt9j/20230605095047-484284.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import urllib.request\nassert(urllib.request.urlopen("http://commonwl.org").code == 200)\n\'\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/networkaccess.cwl:6:1: checking field \'requirements\'\ntests/wf/networkaccess.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#NetworkAccess\'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/networkaccess-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/networkaccess-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/NetworkAccess\'\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job networkaccess.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\nDEBUG cwltool:command_line_tool.py:988 [job networkaccess.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job networkaccess.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job networkaccess.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "valueFrom": "import urllib.request\\nassert(urllib.request.urlopen(\\"http://commonwl.org\\").code == 200)\\n",\n "position": [\n 0,\n 1\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job networkaccess.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job networkaccess.cwl] /private/tmp/docker_tmp75dfw90k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp75dfw90k,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp2jf3vw_z,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp1vsmbt9j/20230605095047-484284.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import urllib.request\nassert(urllib.request.urlopen("http://commonwl.org").code == 200)\n\'\nINFO cwltool:job.py:905 [job networkaccess.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job networkaccess.cwl] completed success\nDEBUG cwltool:job.py:422 [job networkaccess.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job networkaccess.cwl] Removing input staging directory /private/tmp/docker_tmp9kgn1gg0\nDEBUG cwltool:job.py:454 [job networkaccess.cwl] Removing temporary directory /private/tmp/docker_tmp2jf3vw_z\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp75dfw90k\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/networkaccess.cwl:6:1: checking field \'requirements\'\ntests/wf/networkaccess.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#NetworkAccess\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/networkaccess-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/networkaccess-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/NetworkAccess\'')], 'duration': 3.5653393000002325, 'start': 1685951446.647063, 'stop': 1685951450.2123148, '$report_type': 'TestReport', 'item_index': 376, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_require_prefix_networkaccess', 'location': ('tests/test_ext.py', 234, 'test_require_prefix_networkaccess'), 'keywords': {'test_require_prefix_networkaccess': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', '[worker-gw2] received command runtests {\'indices\': [497, 498, 499, 500, 501, 502, 503, 504]}\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] /private/tmp/docker_tmp75dfw90k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp75dfw90k,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp2jf3vw_z,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp1vsmbt9j/20230605095047-484284.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import urllib.request\nassert(urllib.request.urlopen("http://commonwl.org").code == 200)\n\'\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job networkaccess.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/networkaccess.cwl:6:1: checking field \'requirements\'\ntests/wf/networkaccess.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#NetworkAccess\'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/networkaccess-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/networkaccess-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/NetworkAccess\'\x1b[0m\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job networkaccess.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\nDEBUG cwltool:command_line_tool.py:988 [job networkaccess.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job networkaccess.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job networkaccess.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "valueFrom": "import urllib.request\\nassert(urllib.request.urlopen(\\"http://commonwl.org\\").code == 200)\\n",\n "position": [\n 0,\n 1\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job networkaccess.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job networkaccess.cwl] /private/tmp/docker_tmp75dfw90k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp75dfw90k,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp2jf3vw_z,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp1vsmbt9j/20230605095047-484284.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import urllib.request\nassert(urllib.request.urlopen("http://commonwl.org").code == 200)\n\'\nINFO cwltool:job.py:905 [job networkaccess.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job networkaccess.cwl] completed success\nDEBUG cwltool:job.py:422 [job networkaccess.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job networkaccess.cwl] Removing input staging directory /private/tmp/docker_tmp9kgn1gg0\nDEBUG cwltool:job.py:454 [job networkaccess.cwl] Removing temporary directory /private/tmp/docker_tmp2jf3vw_z\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp75dfw90k\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/networkaccess.cwl:6:1: checking field \'requirements\'\ntests/wf/networkaccess.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#NetworkAccess\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/networkaccess-fail.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/networkaccess-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/networkaccess-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/NetworkAccess\'')], 'duration': 0.0005908630000703852, 'start': 1685951450.2137191, 'stop': 1685951450.2143118, '$report_type': 'TestReport', 'item_index': 376, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_require_prefix_networkaccess - location: ('tests/test_ext.py', 234, 'test_require_prefix_networkaccess') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_ext.py::test_require_prefix_workreuse - location: ('tests/test_ext.py', 241, 'test_require_prefix_workreuse') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_require_prefix_workreuse', 'location': ('tests/test_ext.py', 241, 'test_require_prefix_workreuse'), 'keywords': {'test_require_prefix_workreuse': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001844295999944734, 'start': 1685951450.21582, 'stop': 1685951450.2176661, '$report_type': 'TestReport', 'item_index': 377, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters8-result8]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters8-result8]'), 'keywords': {'test_overrides[parameters8-result8]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters8-result8': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\'\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.0-dev1.cwl] /private/tmp/docker_tmpx8gydkjw$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmpx8gydkjw/cwl.output.json\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.0-dev1.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml",\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env-tool_v1.1.0-dev1.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool_v1.1.0-dev1.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool_v1.1.0-dev1.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool_v1.1.0-dev1.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo {\\\\\\"value\\\\\\": \\\\\\"$TEST_ENV\\\\\\"}"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool_v1.1.0-dev1.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool_v1.1.0-dev1.cwl] /private/tmp/docker_tmpx8gydkjw$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmpx8gydkjw/cwl.output.json\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:1222 Raw output from /private/tmp/docker_tmpx8gydkjw/cwl.output.json: {\n "value": "hello test env"\n}\nINFO cwltool:job.py:419 [job env-tool_v1.1.0-dev1.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool_v1.1.0-dev1.cwl] outputs {\n "value": "hello test env"\n}\nDEBUG cwltool:job.py:446 [job env-tool_v1.1.0-dev1.cwl] Removing input staging directory /private/tmp/docker_tmpy3kullbt\nDEBUG cwltool:job.py:454 [job env-tool_v1.1.0-dev1.cwl] Removing temporary directory /private/tmp/docker_tmpkbnw1n9q\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpx8gydkjw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7702155999995739, 'start': 1685951450.0139031, 'stop': 1685951450.7841, '$report_type': 'TestReport', 'item_index': 475, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides[parameters8-result8]', 'location': ('tests/test_override.py', 76, 'test_overrides[parameters8-result8]'), 'keywords': {'test_overrides[parameters8-result8]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters8-result8': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\'\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.0-dev1.cwl] /private/tmp/docker_tmpx8gydkjw$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmpx8gydkjw/cwl.output.json\n\x1b[1;30mINFO\x1b[0m [job env-tool_v1.1.0-dev1.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\' to \'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default.yaml",\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env-tool_v1.1.0-dev1.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool_v1.1.0-dev1.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool_v1.1.0-dev1.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool_v1.1.0-dev1.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/bash"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo {\\\\\\"value\\\\\\": \\\\\\"$TEST_ENV\\\\\\"}"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool_v1.1.0-dev1.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool_v1.1.0-dev1.cwl] /private/tmp/docker_tmpx8gydkjw$ /bin/bash \\\n -c \\\n \'echo {\\"value\\": \\"$TEST_ENV\\"}\' > /private/tmp/docker_tmpx8gydkjw/cwl.output.json\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:1222 Raw output from /private/tmp/docker_tmpx8gydkjw/cwl.output.json: {\n "value": "hello test env"\n}\nINFO cwltool:job.py:419 [job env-tool_v1.1.0-dev1.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool_v1.1.0-dev1.cwl] outputs {\n "value": "hello test env"\n}\nDEBUG cwltool:job.py:446 [job env-tool_v1.1.0-dev1.cwl] Removing input staging directory /private/tmp/docker_tmpy3kullbt\nDEBUG cwltool:job.py:454 [job env-tool_v1.1.0-dev1.cwl] Removing temporary directory /private/tmp/docker_tmpkbnw1n9q\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpx8gydkjw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005138289998285472, 'start': 1685951450.785271, 'stop': 1685951450.7857862, '$report_type': 'TestReport', 'item_index': 475, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides[parameters8-result8] - location: ('tests/test_override.py', 76, 'test_overrides[parameters8-result8]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1] - location: ('tests/test_override.py', 119, 'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]'), 'keywords': {'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005757640001320397, 'start': 1685951450.787252, 'stop': 1685951450.787829, '$report_type': 'TestReport', 'item_index': 476, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\uadf8\\ub798\\ud504]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]'), 'keywords': {'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "그래프",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmplyn4vznq\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test"\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/script\nDEBUG cwltool:command_line_tool.py:988 [job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\uadf8\\ub798\\ud504"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test",\n "dirname": "/private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script] initial work dir {}\nINFO cwltool:job.py:266 [job script] /private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script] completed success\nDEBUG cwltool:job.py:422 [job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\nDEBUG cwltool:job.py:454 [job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplyn4vznq\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7623934020002707, 'start': 1685951450.142199, 'stop': 1685951450.9045749, '$report_type': 'TestReport', 'item_index': 505, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish 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/private/tmp/docker_tmplyn4vznq$ cat \\\n /private/tmp/docker_tmpzos45i9w/stg34896971-6ea3-4986-8887-483b91a99a01/test > /private/tmp/docker_tmplyn4vznq/그래프\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script] completed success\nDEBUG cwltool:job.py:422 [job script] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmplyn4vznq/%EA%B7%B8%EB%9E%98%ED%94%84",\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script] Removing input staging directory /private/tmp/docker_tmpzos45i9w\nDEBUG cwltool:job.py:454 [job script] Removing temporary directory /private/tmp/docker_tmppa75hoql\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplyn4vznq/그래프 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__0/outdir/그래프\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplyn4vznq\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008543869998902665, 'start': 1685951450.9057658, 'stop': 1685951450.906623, '$report_type': 'TestReport', 'item_index': 505, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\uadf8\ub798\ud504] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\uadf8\\ub798\\ud504]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]'), 'keywords': {'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0022306440005195327, 'start': 1685951450.908751, 'stop': 1685951450.910984, '$report_type': 'TestReport', 'item_index': 506, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_output', 'location': ('tests/test_provenance.py', 160, 'test_secondary_files_output'), 'keywords': {'test_secondary_files_output': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "file1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt",\n "basename": "f.txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size",\n "class": "File",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter",\n "class": "File",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwjr18vof/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmptl8e6f9x$ /bin/sh \\\n -c \\\n echo "abc" > f.txt; echo "3" > f.txt.size; echo "a" > f.txt.firstletter; echo "a,b,c" > f.csv; echo "1,2,3" > f.csv.columns; echo "ignored" > f.txt.ignoreme;\n\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: dbf5eef1a93906a11f500e9f6a94d8f65d608284 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: ef33879db2f10ebed5a6b3bc3a12dea6059dfd003dfff5a196e5f85eaadf2ba0 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 833b03ecbda05d8947f87e51d289011e1d071e5e9a02a7d74e2f7e1d8e99a937f05b32f4a4112179a0bd8d635922da1de2ce6915597922a9e1580d2207dc386f workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwjr18vof/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/9ce15f63-7b5f-4e14-9592-43f785c1656c as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "echo \\"abc\\" > f.txt; echo \\"3\\" > f.txt.size; echo \\"a\\" > f.txt.firstletter; echo \\"a,b,c\\" > f.csv; echo \\"1,2,3\\" > f.csv.columns; echo \\"ignored\\" > f.txt.ignoreme;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmptl8e6f9x$ /bin/sh \\\n -c \\\n echo "abc" > f.txt; echo "3" > f.txt.size; echo "a" > f.txt.firstletter; echo "a,b,c" > f.csv; echo "1,2,3" > f.csv.columns; echo "ignored" > f.txt.ignoreme;\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 03cfd743661f07975fa2f1220c5194cbaff48451 data/03/03cfd743661f07975fa2f1220c5194cbaff48451\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: a3db5c13ff90a36963278c6a39e4ee3c22e2a436 data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 3f786850e387550fdab836ed7e6dc881de23001b data/3f/3f786850e387550fdab836ed7e6dc881de23001b\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 0f8ae3519acea73e158af005549dc58e8eb5d0df data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 593706831ae6760bd8b9a98b9204880a72f808c6 data/59/593706831ae6760bd8b9a98b9204880a72f808c6\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/59/593706831ae6760bd8b9a98b9204880a72f808c6\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/59/593706831ae6760bd8b9a98b9204880a72f808c6\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n },\n "file1csv": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "basename": "f.csv",\n "nameroot": "f",\n "nameext": ".csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "secondaryFiles": [\n {\n "basename": "f.csv.columns",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv.columns",\n "class": "File",\n "nameroot": "f.csv",\n "nameext": ".columns",\n "checksum": "sha1$593706831ae6760bd8b9a98b9204880a72f808c6",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:cbcd92ce-fff6-4c77-a6c7-d6e90f6ecef0"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:ea8d845d-f973-4952-b50d-2915b1ddb73d"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/file1csv": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "basename": "f.csv",\n "nameroot": "f",\n "nameext": ".csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "secondaryFiles": [\n {\n "basename": "f.csv.columns",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv.columns",\n "class": "File",\n "nameroot": "f.csv",\n "nameext": ".columns",\n "checksum": "sha1$593706831ae6760bd8b9a98b9204880a72f808c6",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:cbcd92ce-fff6-4c77-a6c7-d6e90f6ecef0"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:ea8d845d-f973-4952-b50d-2915b1ddb73d"\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n }\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpu3a4n93r\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpx5c78te_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt.size to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt.firstletter to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.csv to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp189hqv35\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptl8e6f9x\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: fa92c9177177f936cdd0212b7b26446ea28cda99 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: e8de14296bbe27af77d4f898752453ca0034c6e198bc62d313d5a579e1663daf metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: d01a3442648b65bf2246d43c7d33a60bf8b48c4ea713be0baaa70d16b6b7d8e008040c6329389c9dd5f095167440bfeb6af99df72e95e0ad4907eb6316c07210 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 71a7df0e199fb2b9fd211d58ffd07a30fb7c63e2 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 74355e4ddd99d82d89f79a29c332af5e3ca949b5e8d7e26ea0b2ceec527a3a94 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: e3750188dcebc789f166c32c097e9fa2a2fe93ab80a2c81dcae3a2bb87031d6a436e73e8362cd31cf4643d0454a813b27bf784b36b0082dca16920046439b7e1 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 176d0de5b0e0a92d27b39c355a386e3dc8497d18 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: de346266db74f4c6868e657e65e0491bb1053623ef10893e2ef289ae72bb79bf metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 5e470078ea0bc32960168987f8879cd4aea325c19979cd6f62d531892033051c64dff7cf33a72563a8ea7afd6cb51f833ca8da8fb4aa0ad540aff8955739b8ed metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 7982b196c67c4c3a50cc5da7613a0adc7c5424c5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: efda73edb11c091d10d96ba2d0a6bdfc46f110e30ea732beecb21ae2f3be6e94 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 7b86ec13244c7a658df1e8bc3f86ae8c6fa6d8b02fca043d61fb390190dc126110f7f5eb644dbe9dc48f3808b6e3fb52a6aab75dc797d7f34e72ad0ab5f45d8c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: bf4bd610c999085234872c8249d99c9de12b411c metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: fae8f3f405ca5c887e358d3814e056171235190eadc776a5317704828023746a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 37102c6ced82c58acc6241193c569132fd3e2dcfab1e201746c0bbd401a65a65c77d81de9d3f5745cf8c74dc153ab872097ad0983c4f6e77ca5370241c017b3a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 3687158ff1b66b5561e0b43be70b77107f40ee0d metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 8405cb03c17012e3e3733e54ea1feac3ecd232d0e767ed6536ac32a65fedb970 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: ef891c640d1e6f76eb404fb08cea726d4ad1ed73f482796d8162fd8b5e10531dce2708a95d0f63b4b3cda1893ce92a5a6c4bdbf1200952e8db9662c8318ef0b5 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\', \'basename\': \'f.txt\', \'nameroot\': \'f\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$03cfd743661f07975fa2f1220c5194cbaff48451\', \'size\': 4, \'secondaryFiles\': [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}], \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\', \'basename\': \'f.txt\', \'nameroot\': \'f\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$03cfd743661f07975fa2f1220c5194cbaff48451\', \'size\': 4, \'secondaryFiles\': [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}], \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt.size\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .size\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt.firstletter\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .firstletter\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.csv\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .csv\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 6\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 3ffb077462a7366ed56387657cf594c9b0d1b2c7 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 1444a80bd29d7069612ee7da6e0827aa7753a7bbbe2aa2630dc7f5432a4afdf9 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 5dbcb8f2cae6ccaa2629dfaa958aa306d53f9c8b9dd9f4b6c0d0606cbc049234c5b980005888ea539e94878a4309913e66370e8acebd1be4f35431fd8a3b5a9d workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: c5748d1251c37c7867c3c1d862c07b9878312eaa snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 67a63dbce041f71b377337196622308a9878245770761c1f262f81c4f4947def snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: d6a23fcdcb8ad33277e282d1bbd6fa38b8e50acb9daed31c45d92cbd61eacdb6445a0f2a22b01d78cf461962606db623e3dbcf9dbfa25cd44257b29b34a6a995 snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 537134b46bec1dfd4f639062130613c13a21bb65 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: a7d8e1cddfa8aaf793a2bba0d6293c722c561ec47575d81ffeb98914f0683848 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 8072951e1ca5d3fea48562d150dfce861b21dd5cce224f15b3ee21810e7fef677b41b9cff70bbbcf7cc9ad3246e4664295778a9c25ebbb1294febfc3c72894e3 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 0498f7f4009a5a84331e8b24fb83650d30af83f0 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 7b7f4ea36d4cdac950c799f82d0fa998385ce568888d640d77383d932914cbfe metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 3354b68c419ef9993f09b8f084a51a301bc44796df1f8535af054070a5b3d2b8e4d4e6579e58eb000c302a8ae10337ab989120f97f6734f3a11c0c5005b9b4ae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 688538bd7ce28063bf00184b1b965ba4aafece24 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 1c399bf2f5bd0fe13f29342156ec3a743516ab188f2b4c711fb37651ae68a222 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 25c66d4ed947eca4529f5722e7df143e89d14da48cbe3c502f98efd1c89571335c0e9392606635a402b04ac46b369a40c05a6c089278dec1872b42a821a2c213 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance')], 'duration': 1.1671647269995447, 'start': 1685951449.93065, 'stop': 1685951451.097787, '$report_type': 'TestReport', 'item_index': 530, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_output', 'location': ('tests/test_provenance.py', 160, 'test_secondary_files_output'), 'keywords': {'test_secondary_files_output': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "file1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt",\n "basename": "f.txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size",\n "class": "File",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter",\n "class": "File",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwjr18vof/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step step1\n\x1b[1;30mINFO\x1b[0m [step step1] start\n\x1b[1;30mINFO\x1b[0m [job step1] /private/tmp/docker_tmptl8e6f9x$ /bin/sh \\\n -c \\\n echo "abc" > f.txt; echo "3" > f.txt.size; echo "a" > f.txt.firstletter; echo "a,b,c" > f.csv; echo "1,2,3" > f.csv.columns; echo "ignored" > f.txt.ignoreme;\n\n\x1b[1;30mINFO\x1b[0m [job step1] completed success\n\x1b[1;30mINFO\x1b[0m [step step1] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: dbf5eef1a93906a11f500e9f6a94d8f65d608284 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: ef33879db2f10ebed5a6b3bc3a12dea6059dfd003dfff5a196e5f85eaadf2ba0 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 833b03ecbda05d8947f87e51d289011e1d071e5e9a02a7d74e2f7e1d8e99a937f05b32f4a4112179a0bd8d635922da1de2ce6915597922a9e1580d2207dc386f workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwjr18vof/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/9ce15f63-7b5f-4e14-9592-43f785c1656c as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "echo \\"abc\\" > f.txt; echo \\"3\\" > f.txt.size; echo \\"a\\" > f.txt.firstletter; echo \\"a,b,c\\" > f.csv; echo \\"1,2,3\\" > f.csv.columns; echo \\"ignored\\" > f.txt.ignoreme;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job step1] initial work dir {}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmptl8e6f9x$ /bin/sh \\\n -c \\\n echo "abc" > f.txt; echo "3" > f.txt.size; echo "a" > f.txt.firstletter; echo "a,b,c" > f.csv; echo "1,2,3" > f.csv.columns; echo "ignored" > f.txt.ignoreme;\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 03cfd743661f07975fa2f1220c5194cbaff48451 data/03/03cfd743661f07975fa2f1220c5194cbaff48451\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: a3db5c13ff90a36963278c6a39e4ee3c22e2a436 data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 3f786850e387550fdab836ed7e6dc881de23001b data/3f/3f786850e387550fdab836ed7e6dc881de23001b\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 0f8ae3519acea73e158af005549dc58e8eb5d0df data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/manifest-sha1.txt: 593706831ae6760bd8b9a98b9204880a72f808c6 data/59/593706831ae6760bd8b9a98b9204880a72f808c6\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/data/59/593706831ae6760bd8b9a98b9204880a72f808c6\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/59/593706831ae6760bd8b9a98b9204880a72f808c6\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n },\n "file1csv": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "basename": "f.csv",\n "nameroot": "f",\n "nameext": ".csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "secondaryFiles": [\n {\n "basename": "f.csv.columns",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv.columns",\n "class": "File",\n "nameroot": "f.csv",\n "nameext": ".columns",\n "checksum": "sha1$593706831ae6760bd8b9a98b9204880a72f808c6",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:cbcd92ce-fff6-4c77-a6c7-d6e90f6ecef0"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:ea8d845d-f973-4952-b50d-2915b1ddb73d"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf-out.cwl#step1/file1csv": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "basename": "f.csv",\n "nameroot": "f",\n "nameext": ".csv",\n "class": "File",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "secondaryFiles": [\n {\n "basename": "f.csv.columns",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv.columns",\n "class": "File",\n "nameroot": "f.csv",\n "nameext": ".columns",\n "checksum": "sha1$593706831ae6760bd8b9a98b9204880a72f808c6",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:cbcd92ce-fff6-4c77-a6c7-d6e90f6ecef0"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:ea8d845d-f973-4952-b50d-2915b1ddb73d"\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "file1": {\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt",\n "basename": "f.txt",\n "nameroot": "f",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$03cfd743661f07975fa2f1220c5194cbaff48451",\n "size": 4,\n "secondaryFiles": [\n {\n "basename": "f.txt.size",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.size",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".size",\n "checksum": "sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007"\n },\n {\n "basename": "f.txt.firstletter",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.txt.firstletter",\n "class": "File",\n "nameroot": "f.txt",\n "nameext": ".firstletter",\n "checksum": "sha1$3f786850e387550fdab836ed7e6dc881de23001b",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0"\n },\n {\n "basename": "f.csv",\n "location": "file:///private/tmp/docker_tmptl8e6f9x/f.csv",\n "class": "File",\n "nameroot": "f",\n "nameext": ".csv",\n "checksum": "sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e"\n }\n ],\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:3c355832-5867-44ac-906e-22801493e3aa"\n }\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpu3a4n93r\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmpx5c78te_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt.size to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.txt.firstletter to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptl8e6f9x/f.csv to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp189hqv35\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptl8e6f9x\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: fa92c9177177f936cdd0212b7b26446ea28cda99 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: e8de14296bbe27af77d4f898752453ca0034c6e198bc62d313d5a579e1663daf metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: d01a3442648b65bf2246d43c7d33a60bf8b48c4ea713be0baaa70d16b6b7d8e008040c6329389c9dd5f095167440bfeb6af99df72e95e0ad4907eb6316c07210 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 71a7df0e199fb2b9fd211d58ffd07a30fb7c63e2 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 74355e4ddd99d82d89f79a29c332af5e3ca949b5e8d7e26ea0b2ceec527a3a94 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: e3750188dcebc789f166c32c097e9fa2a2fe93ab80a2c81dcae3a2bb87031d6a436e73e8362cd31cf4643d0454a813b27bf784b36b0082dca16920046439b7e1 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 176d0de5b0e0a92d27b39c355a386e3dc8497d18 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: de346266db74f4c6868e657e65e0491bb1053623ef10893e2ef289ae72bb79bf metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 5e470078ea0bc32960168987f8879cd4aea325c19979cd6f62d531892033051c64dff7cf33a72563a8ea7afd6cb51f833ca8da8fb4aa0ad540aff8955739b8ed metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 7982b196c67c4c3a50cc5da7613a0adc7c5424c5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: efda73edb11c091d10d96ba2d0a6bdfc46f110e30ea732beecb21ae2f3be6e94 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 7b86ec13244c7a658df1e8bc3f86ae8c6fa6d8b02fca043d61fb390190dc126110f7f5eb644dbe9dc48f3808b6e3fb52a6aab75dc797d7f34e72ad0ab5f45d8c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: bf4bd610c999085234872c8249d99c9de12b411c metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: fae8f3f405ca5c887e358d3814e056171235190eadc776a5317704828023746a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 37102c6ced82c58acc6241193c569132fd3e2dcfab1e201746c0bbd401a65a65c77d81de9d3f5745cf8c74dc153ab872097ad0983c4f6e77ca5370241c017b3a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 3687158ff1b66b5561e0b43be70b77107f40ee0d metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 8405cb03c17012e3e3733e54ea1feac3ecd232d0e767ed6536ac32a65fedb970 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: ef891c640d1e6f76eb404fb08cea726d4ad1ed73f482796d8162fd8b5e10531dce2708a95d0f63b4b3cda1893ce92a5a6c4bdbf1200952e8db9662c8318ef0b5 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\', \'basename\': \'f.txt\', \'nameroot\': \'f\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$03cfd743661f07975fa2f1220c5194cbaff48451\', \'size\': 4, \'secondaryFiles\': [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}], \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt\', \'basename\': \'f.txt\', \'nameroot\': \'f\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$03cfd743661f07975fa2f1220c5194cbaff48451\', \'size\': 4, \'secondaryFiles\': [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}], \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/03/03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$03cfd743661f07975fa2f1220c5194cbaff48451\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}, {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}, {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.txt.size\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.size\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.size\', \'checksum\': \'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt.size\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/a3/a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .size\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:dbdf78a3-2f1d-43e4-8a71-f4575e566007\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.txt.firstletter\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.txt.firstletter\', \'class\': \'File\', \'nameroot\': \'f.txt\', \'nameext\': \'.firstletter\', \'checksum\': \'sha1$3f786850e387550fdab836ed7e6dc881de23001b\', \'size\': 2, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt.firstletter\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/3f/3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .firstletter\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$3f786850e387550fdab836ed7e6dc881de23001b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:7fc71820-8409-4c1c-9473-47dddec446f0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'basename\': \'f.csv\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/cwltool-run/f.csv\', \'class\': \'File\', \'nameroot\': \'f\', \'nameext\': \'.csv\', \'checksum\': \'sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f.csv\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0f/0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: f\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .csv\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0f8ae3519acea73e158af005549dc58e8eb5d0df\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 6\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:acd0037c-e100-4137-aa4c-9329d4d3c87e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:3c355832-5867-44ac-906e-22801493e3aa\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 3ffb077462a7366ed56387657cf594c9b0d1b2c7 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 1444a80bd29d7069612ee7da6e0827aa7753a7bbbe2aa2630dc7f5432a4afdf9 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 5dbcb8f2cae6ccaa2629dfaa958aa306d53f9c8b9dd9f4b6c0d0606cbc049234c5b980005888ea539e94878a4309913e66370e8acebd1be4f35431fd8a3b5a9d workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: c5748d1251c37c7867c3c1d862c07b9878312eaa snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 67a63dbce041f71b377337196622308a9878245770761c1f262f81c4f4947def snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: d6a23fcdcb8ad33277e282d1bbd6fa38b8e50acb9daed31c45d92cbd61eacdb6445a0f2a22b01d78cf461962606db623e3dbcf9dbfa25cd44257b29b34a6a995 snapshot/sec-wf-out.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 537134b46bec1dfd4f639062130613c13a21bb65 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: a7d8e1cddfa8aaf793a2bba0d6293c722c561ec47575d81ffeb98914f0683848 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 8072951e1ca5d3fea48562d150dfce861b21dd5cce224f15b3ee21810e7fef677b41b9cff70bbbcf7cc9ad3246e4664295778a9c25ebbb1294febfc3c72894e3 metadata/logs/engine.c25c54fa-0312-46fd-8108-9cc74b3ab7e1.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 0498f7f4009a5a84331e8b24fb83650d30af83f0 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 7b7f4ea36d4cdac950c799f82d0fa998385ce568888d640d77383d932914cbfe metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 3354b68c419ef9993f09b8f084a51a301bc44796df1f8535af054070a5b3d2b8e4d4e6579e58eb000c302a8ae10337ab989120f97f6734f3a11c0c5005b9b4ae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha1.txt: 688538bd7ce28063bf00184b1b965ba4aafece24 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha256.txt: 1c399bf2f5bd0fe13f29342156ec3a743516ab188f2b4c711fb37651ae68a222 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f/tagmanifest-sha512.txt: 25c66d4ed947eca4529f5722e7df143e89d14da48cbe3c502f98efd1c89571335c0e9392606635a402b04ac46b369a40c05a6c089278dec1872b42a821a2c213 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/toj4uh3f\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_secondary_files_output0/provenance')], 'duration': 0.000757134000195947, 'start': 1685951451.099516, 'stop': 1685951451.100275, '$report_type': 'TestReport', 'item_index': 530, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_secondary_files_output - location: ('tests/test_provenance.py', 160, 'test_secondary_files_output') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - when: runtest - nodeid: tests/test_provenance.py::test_secondary_files_output - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_directory_workflow - location: ('tests/test_provenance.py', 169, 'test_directory_workflow') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow', 'location': ('tests/test_provenance.py', 169, 'test_directory_workflow'), 'keywords': {'test_directory_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001610086999789928, 'start': 1685951451.102933, 'stop': 1685951451.104544, '$report_type': 'TestReport', 'item_index': 531, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]'), 'keywords': {'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/formattest.cwl-tests/wf/formattest-job.json-True': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:49]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\n\x1b[1;30mINFO\x1b[0m [job formattest.cwl] /private/tmp/docker_tmp9uzslvog$ rev \\\n /private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt > /private/tmp/docker_tmp9uzslvog/output.txt\n\x1b[1;30mINFO\x1b[0m [job formattest.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck#main\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "dirname": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main] /private/tmp/docker_tmpr6g49v7h$ rev \\\n /private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt > /private/tmp/docker_tmpr6g49v7h/output.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpr6g49v7h/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] Removing input staging directory /private/tmp/docker_tmp3uoblnx6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] Removing temporary directory /private/tmp/docker_tmpekbfudg1\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpr6g49v7h/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpr6g49v7h\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job formattest.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\nDEBUG cwltool:command_line_tool.py:988 [job formattest.cwl] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job formattest.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job formattest.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt",\n "dirname": "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job formattest.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job formattest.cwl] /private/tmp/docker_tmp9uzslvog$ rev \\\n /private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt > /private/tmp/docker_tmp9uzslvog/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job formattest.cwl] completed success\nDEBUG cwltool:job.py:422 [job formattest.cwl] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp9uzslvog/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job formattest.cwl] Removing input staging directory /private/tmp/docker_tmpko9q_21s\nDEBUG cwltool:job.py:454 [job formattest.cwl] Removing temporary directory /private/tmp/docker_tmp5ylwymyc\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp9uzslvog/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9uzslvog\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\'\nDEBUG cwltool:command_line_tool.py:982 [job main] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck#main\nDEBUG cwltool:command_line_tool.py:988 [job main] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job main] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "dirname": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job main] initial work dir {}\nINFO cwltool:job.py:266 [job main] /private/tmp/docker_tmpr6g49v7h$ rev \\\n /private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt > /private/tmp/docker_tmpr6g49v7h/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main] completed success\nDEBUG cwltool:job.py:422 [job main] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpr6g49v7h/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job main] Removing input staging directory /private/tmp/docker_tmp3uoblnx6\nDEBUG cwltool:job.py:454 [job main] Removing temporary directory /private/tmp/docker_tmpekbfudg1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpr6g49v7h/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr6g49v7h\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.5225798010005747, 'start': 1685951449.591155, 'stop': 1685951451.113698, '$report_type': 'TestReport', 'item_index': 493, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]', 'location': ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]'), 'keywords': {'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'tests/wf/formattest.cwl-tests/wf/formattest-job.json-True': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:49]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\n\x1b[1;30mINFO\x1b[0m [job formattest.cwl] /private/tmp/docker_tmp9uzslvog$ rev \\\n /private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt > /private/tmp/docker_tmp9uzslvog/output.txt\n\x1b[1;30mINFO\x1b[0m [job formattest.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck#main\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "dirname": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main] /private/tmp/docker_tmpr6g49v7h$ rev \\\n /private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt > /private/tmp/docker_tmpr6g49v7h/output.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpr6g49v7h/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] Removing input staging directory /private/tmp/docker_tmp3uoblnx6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main] Removing temporary directory /private/tmp/docker_tmpekbfudg1\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpr6g49v7h/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpr6g49v7h\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job formattest.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl\nDEBUG cwltool:command_line_tool.py:988 [job formattest.cwl] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job formattest.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job formattest.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt",\n "dirname": "/private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job formattest.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job formattest.cwl] /private/tmp/docker_tmp9uzslvog$ rev \\\n /private/tmp/docker_tmpko9q_21s/stga3c4e060-f3fb-4544-b9a4-5344689f176c/whale.txt > /private/tmp/docker_tmp9uzslvog/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job formattest.cwl] completed success\nDEBUG cwltool:job.py:422 [job formattest.cwl] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp9uzslvog/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job formattest.cwl] Removing input staging directory /private/tmp/docker_tmpko9q_21s\nDEBUG cwltool:job.py:454 [job formattest.cwl] Removing temporary directory /private/tmp/docker_tmp5ylwymyc\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp9uzslvog/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp9uzslvog\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\' to \'file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck\'\nDEBUG cwltool:command_line_tool.py:982 [job main] initializing from file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwl4us_ck#main\nDEBUG cwltool:command_line_tool.py:988 [job main] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job main] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "http://edamontology.org/format_2330",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt",\n "dirname": "/private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job main] initial work dir {}\nINFO cwltool:job.py:266 [job main] /private/tmp/docker_tmpr6g49v7h$ rev \\\n /private/tmp/docker_tmp3uoblnx6/stg2c783dd2-c85d-4f8c-a676-ec50e68ee224/whale.txt > /private/tmp/docker_tmpr6g49v7h/output.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main] completed success\nDEBUG cwltool:job.py:422 [job main] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpr6g49v7h/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "format": "http://edamontology.org/format_2330",\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job main] Removing input staging directory /private/tmp/docker_tmp3uoblnx6\nDEBUG cwltool:job.py:454 [job main] Removing temporary directory /private/tmp/docker_tmpekbfudg1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpr6g49v7h/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_packed_workflow_execution1/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr6g49v7h\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007574420005767024, 'start': 1685951451.114835, 'stop': 1685951451.115593, '$report_type': 'TestReport', 'item_index': 493, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True] - location: ('tests/test_pack.py', 187, 'test_packed_workflow_execution[tests/wf/formattest.cwl-tests/wf/formattest-job.json-True]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_parallel.py::test_sequential_workflow - location: ('tests/test_parallel.py', 10, 'test_sequential_workflow') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_parallel.py::test_sequential_workflow', 'location': ('tests/test_parallel.py', 10, 'test_sequential_workflow'), 'keywords': {'test_sequential_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013370579999900656, 'start': 1685951451.117016, 'stop': 1685951451.1183538, '$report_type': 'TestReport', 'item_index': 494, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]'), 'keywords': {'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool.cwl'\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\n`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1")], 'duration': 0.7309547619997829, 'start': 1685951450.788568, 'stop': 1685951451.519506, '$report_type': 'TestReport', 'item_index': 476, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]'), 'keywords': {'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool.cwl'\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\n`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1")], 'duration': 0.00033288000031461706, 'start': 1685951451.519996, 'stop': 1685951451.52033, '$report_type': 'TestReport', 'item_index': 476, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1] - location: ('tests/test_override.py', 119, 'test_overrides_fails[parameters0-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.] - location: ('tests/test_override.py', 119, "test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]") - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0010089769994010567, 'start': 1685951451.52194, 'stop': 1685951451.522951, '$report_type': 'TestReport', 'item_index': 477, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nVersion 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.")], 'duration': 0.026144765000026382, 'start': 1685951451.524121, 'stop': 1685951451.550267, '$report_type': 'TestReport', 'item_index': 477, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': "tests/test_override.py::test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]", 'location': ('tests/test_override.py', 119, "test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]"), 'keywords': {"test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]": 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, "parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.": 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_v1.1.0-dev1.cwl'\nERROR cwltool:main.py:1208 Tool definition failed validation:\nVersion 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.")], 'duration': 0.000790431000496028, 'start': 1685951451.551027, 'stop': 1685951451.55182, '$report_type': 'TestReport', 'item_index': 477, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.] - location: ('tests/test_override.py', 119, "test_overrides_fails[parameters1-Version 'v1.1.0-dev1' is a development or deprecated version.\\n Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to enable support for development and deprecated versions.]") - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_override.py::test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.] - location: ('tests/test_override.py', 119, 'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]'), 'keywords': {'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006940140001461259, 'start': 1685951451.554448, 'stop': 1685951451.5551438, '$report_type': 'TestReport', 'item_index': 478, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]'), 'keywords': {'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml'\nERROR cwltool:main.py:1208 Tool definition failed validation:\n`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.")], 'duration': 0.027587419000155933, 'start': 1685951451.555978, 'stop': 1685951451.5835662, '$report_type': 'TestReport', 'item_index': 478, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_override.py::test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]', 'location': ('tests/test_override.py', 119, 'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]'), 'keywords': {'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.': 1, 'test_override.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml' to 'file:///Users/jasperk/gitlab/cwltool/tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml'\nERROR cwltool:main.py:1208 Tool definition failed validation:\n`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.")], 'duration': 0.0007339860003412468, 'start': 1685951451.5840719, 'stop': 1685951451.584807, '$report_type': 'TestReport', 'item_index': 478, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_override.py::test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.] - location: ('tests/test_override.py', 119, 'test_overrides_fails[parameters2-`cwl:requirements` in the input object is not part of CWL v1.0. You can adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to v1.1 or greater.]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_writable_bytes - location: ('tests/test_provenance.py', 664, 'test_writable_bytes') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_writable_bytes', 'location': ('tests/test_provenance.py', 664, 'test_writable_bytes'), 'keywords': {'test_writable_bytes': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u')], 'duration': 0.005912863000048674, 'start': 1685951451.5864651, 'stop': 1685951451.5923798, '$report_type': 'TestReport', 'item_index': 537, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_writable_bytes', 'location': ('tests/test_provenance.py', 664, 'test_writable_bytes'), 'keywords': {'test_writable_bytes': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha256.txt: bb16a101c183c6c35bd53683d04273e214e77926e039369f065b11df84b47c80 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha512.txt: e03ebad752a05a76268c9516807e8564af9a26827485e1e3525b06e1d784437a5e9455f764a9914f1a7b851ebfeab27127a5174955711b7e4fd2bfaa8057bd1b file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha256.txt: 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WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_writable_bytes0/tmpetkn33_u/tagmanifest-sha256.txt: bb16a101c183c6c35bd53683d04273e214e77926e039369f065b11df84b47c80 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to 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- report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_data', 'location': ('tests/test_provenance.py', 670, 'test_data'), 'keywords': {'test_data': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: 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'\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/data/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha1.txt: 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 data/file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha256.txt: 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 data/file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha512.txt: c2bad2223811194582af4d1508ac02cd69eeeeedeeb98d54fcae4dcefb13cc882e7640328206603d3fb9cd5f949a9be0db054dd34fbfa190c498a5fe09750cef data/file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/data/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha1.txt: 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 data/file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha256.txt: 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 data/file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j/manifest-sha512.txt: c2bad2223811194582af4d1508ac02cd69eeeeedeeb98d54fcae4dcefb13cc882e7640328206603d3fb9cd5f949a9be0db054dd34fbfa190c498a5fe09750cef data/file.txt'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_data0/tmpi55j5y4j')], 'duration': 0.002914530999987619, 'start': 1685951451.616121, 'stop': 1685951451.619037, '$report_type': 'TestReport', 'item_index': 538, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_data - location: ('tests/test_provenance.py', 670, 'test_data') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_not_seekable - location: ('tests/test_provenance.py', 684, 'test_not_seekable') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_procgenerator.py::test_missing_enable_ext', 'location': ('tests/test_procgenerator.py', 11, 'test_missing_enable_ext'), 'keywords': {'test_missing_enable_ext': 1, 'test_procgenerator.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw5] received command runtests {'indices': [525, 526, 527, 528, 529]}\n"), ('Captured stdout call', '{}{}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/generator/pytoolgen.cwl:5:1: Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#ProcessGenerator\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking object\n \'tests/wf/generator/pytoolgen.cwl#63b74b39-a071-4257-b29d-255fd3678eff\'\ntests/wf/generator/pytoolgen.cwl:20:3: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmprlvxti83/stg2af42b50-d1e6-4c94-88fd-f39581a3c50f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n true\n ],\n "_:3de4ddb3-d354-49a0-b40e-33b49f9cfcbc": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmpimru1mpg/inp.py",\n "CreateFile",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] /private/tmp/docker_tmpimru1mpg$ python \\\n inp.py > /private/tmp/docker_tmpimru1mpg/main.cwl\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmpimru1mpg/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing input staging directory /private/tmp/docker_tmprlvxti83\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing temporary directory /private/tmp/docker_tmpmsq9o_0c\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpimru1mpg/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpimru1mpg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] {\n "zing": "zipper"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main.cwl] /private/tmp/docker_tmpvu2jo5rk$ echo \\\n zipper\nzipper\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] outputs {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] Removing input staging directory /private/tmp/docker_tmp3wbe2izn\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] Removing temporary directory /private/tmp/docker_tmp3kxlbsg0\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvu2jo5rk\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mINFO\x1b[0m [job 07d993b3-177f-45a0-8789-6297c239ab04] /private/tmp/docker_tmp49cf7jpt$ python \\\n inp.py > /private/tmp/docker_tmp49cf7jpt/main.cwl\n\x1b[1;30mINFO\x1b[0m [job 07d993b3-177f-45a0-8789-6297c239ab04] completed success\n\x1b[1;30mINFO\x1b[0m [job main.cwl_2] /private/tmp/docker_tmpofjjqo7q$ echo \\\n zipper\nzipper\n\x1b[1;30mINFO\x1b[0m [job main.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/generator/pytoolgen.cwl:5:1: Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#ProcessGenerator\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking object\n \'tests/wf/generator/pytoolgen.cwl#63b74b39-a071-4257-b29d-255fd3678eff\'\ntests/wf/generator/pytoolgen.cwl:20:3: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e\nDEBUG cwltool:command_line_tool.py:988 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmprlvxti83/stg2af42b50-d1e6-4c94-88fd-f39581a3c50f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\nDEBUG cwltool:job.py:215 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n true\n ],\n "_:3de4ddb3-d354-49a0-b40e-33b49f9cfcbc": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmpimru1mpg/inp.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] /private/tmp/docker_tmpimru1mpg$ python \\\n inp.py > /private/tmp/docker_tmpimru1mpg/main.cwl\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] completed success\nDEBUG cwltool:job.py:422 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmpimru1mpg/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing input staging directory /private/tmp/docker_tmprlvxti83\nDEBUG cwltool:job.py:454 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing temporary directory /private/tmp/docker_tmpmsq9o_0c\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpimru1mpg/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpimru1mpg\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:982 [job main.cwl] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:command_line_tool.py:988 [job main.cwl] {\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job main.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\nDEBUG cwltool:job.py:215 [job main.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job main.cwl] /private/tmp/docker_tmpvu2jo5rk$ echo \\\n zipper\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main.cwl] completed success\nDEBUG cwltool:job.py:422 [job main.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job main.cwl] Removing input staging directory /private/tmp/docker_tmp3wbe2izn\nDEBUG cwltool:job.py:454 [job main.cwl] Removing temporary directory /private/tmp/docker_tmp3kxlbsg0\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvu2jo5rk\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job 07d993b3-177f-45a0-8789-6297c239ab04] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#07d993b3-177f-45a0-8789-6297c239ab04\nDEBUG cwltool:command_line_tool.py:988 [job 07d993b3-177f-45a0-8789-6297c239ab04] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job 07d993b3-177f-45a0-8789-6297c239ab04] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmpkqg74yut/stg22aa02e0-1fa4-463f-84cf-f80e2705270f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmp49cf7jpt/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmp49cf7jpt/pytoolgen.cwl",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job 07d993b3-177f-45a0-8789-6297c239ab04] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\nDEBUG cwltool:job.py:215 [job 07d993b3-177f-45a0-8789-6297c239ab04] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmp49cf7jpt/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmp49cf7jpt/pytoolgen.cwl",\n "File",\n true\n ],\n "_:899bc3cb-ab75-4248-84a3-8ca71a12aa7b": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmp49cf7jpt/inp.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 07d993b3-177f-45a0-8789-6297c239ab04] /private/tmp/docker_tmp49cf7jpt$ python \\\n inp.py > /private/tmp/docker_tmp49cf7jpt/main.cwl\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job 07d993b3-177f-45a0-8789-6297c239ab04] completed success\nDEBUG cwltool:job.py:422 [job 07d993b3-177f-45a0-8789-6297c239ab04] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmp49cf7jpt/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job 07d993b3-177f-45a0-8789-6297c239ab04] Removing input staging directory /private/tmp/docker_tmpkqg74yut\nDEBUG cwltool:job.py:454 [job 07d993b3-177f-45a0-8789-6297c239ab04] Removing temporary directory /private/tmp/docker_tmpfwqvipwz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp49cf7jpt/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp49cf7jpt\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:982 [job main.cwl_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:command_line_tool.py:988 [job main.cwl_2] {\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job main.cwl_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\nDEBUG cwltool:job.py:215 [job main.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job main.cwl_2] /private/tmp/docker_tmpofjjqo7q$ echo \\\n zipper\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job main.cwl_2] outputs {}\nDEBUG cwltool:job.py:446 [job main.cwl_2] Removing input staging directory /private/tmp/docker_tmp36cpw1ex\nDEBUG cwltool:job.py:454 [job main.cwl_2] Removing temporary directory /private/tmp/docker_tmp35m5sh1r\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpofjjqo7q\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.935050539000258, 'start': 1685951448.686326, 'stop': 1685951451.621305, '$report_type': 'TestReport', 'item_index': 522, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_procgenerator.py::test_missing_enable_ext', 'location': ('tests/test_procgenerator.py', 11, 'test_missing_enable_ext'), 'keywords': {'test_missing_enable_ext': 1, 'test_procgenerator.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw5] received command runtests {'indices': [525, 526, 527, 528, 529]}\n"), ('Captured stdout call', '{}{}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/generator/pytoolgen.cwl:5:1: Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#ProcessGenerator\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking object\n \'tests/wf/generator/pytoolgen.cwl#63b74b39-a071-4257-b29d-255fd3678eff\'\ntests/wf/generator/pytoolgen.cwl:20:3: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmprlvxti83/stg2af42b50-d1e6-4c94-88fd-f39581a3c50f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n true\n ],\n "_:3de4ddb3-d354-49a0-b40e-33b49f9cfcbc": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmpimru1mpg/inp.py",\n "CreateFile",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] /private/tmp/docker_tmpimru1mpg$ python \\\n inp.py > /private/tmp/docker_tmpimru1mpg/main.cwl\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmpimru1mpg/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing input staging directory /private/tmp/docker_tmprlvxti83\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing temporary directory /private/tmp/docker_tmpmsq9o_0c\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpimru1mpg/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpimru1mpg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] {\n "zing": "zipper"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main.cwl] /private/tmp/docker_tmpvu2jo5rk$ echo \\\n zipper\nzipper\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job main.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] outputs {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] Removing input staging directory /private/tmp/docker_tmp3wbe2izn\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job main.cwl] Removing temporary directory /private/tmp/docker_tmp3kxlbsg0\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvu2jo5rk\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\n\x1b[1;30mINFO\x1b[0m [job 07d993b3-177f-45a0-8789-6297c239ab04] /private/tmp/docker_tmp49cf7jpt$ python \\\n inp.py > /private/tmp/docker_tmp49cf7jpt/main.cwl\n\x1b[1;30mINFO\x1b[0m [job 07d993b3-177f-45a0-8789-6297c239ab04] completed success\n\x1b[1;30mINFO\x1b[0m [job main.cwl_2] /private/tmp/docker_tmpofjjqo7q$ echo \\\n zipper\nzipper\n\x1b[1;30mINFO\x1b[0m [job main.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/generator/pytoolgen.cwl:5:1: Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#ProcessGenerator\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\ntests/wf/generator/pytoolgen.cwl:10:1: checking object\n \'tests/wf/generator/pytoolgen.cwl#63b74b39-a071-4257-b29d-255fd3678eff\'\ntests/wf/generator/pytoolgen.cwl:20:3: checking field \'requirements\'\ntests/wf/generator/pytoolgen.cwl:22:5: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#LoadListingRequirement\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e\nDEBUG cwltool:command_line_tool.py:988 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmprlvxti83/stg2af42b50-d1e6-4c94-88fd-f39581a3c50f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\nDEBUG cwltool:job.py:215 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmpimru1mpg/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmpimru1mpg/pytoolgen.cwl",\n "File",\n true\n ],\n "_:3de4ddb3-d354-49a0-b40e-33b49f9cfcbc": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmpimru1mpg/inp.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] /private/tmp/docker_tmpimru1mpg$ python \\\n inp.py > /private/tmp/docker_tmpimru1mpg/main.cwl\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] completed success\nDEBUG cwltool:job.py:422 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmpimru1mpg/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing input staging directory /private/tmp/docker_tmprlvxti83\nDEBUG cwltool:job.py:454 [job cbe71f32-1bb4-4c5a-8633-8a5b0f615e0e] Removing temporary directory /private/tmp/docker_tmpmsq9o_0c\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpimru1mpg/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpimru1mpg\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:982 [job main.cwl] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:command_line_tool.py:988 [job main.cwl] {\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job main.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\nDEBUG cwltool:job.py:215 [job main.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job main.cwl] /private/tmp/docker_tmpvu2jo5rk$ echo \\\n zipper\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main.cwl] completed success\nDEBUG cwltool:job.py:422 [job main.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job main.cwl] Removing input staging directory /private/tmp/docker_tmp3wbe2izn\nDEBUG cwltool:job.py:454 [job main.cwl] Removing temporary directory /private/tmp/docker_tmp3kxlbsg0\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvu2jo5rk\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job 07d993b3-177f-45a0-8789-6297c239ab04] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl#07d993b3-177f-45a0-8789-6297c239ab04\nDEBUG cwltool:command_line_tool.py:988 [job 07d993b3-177f-45a0-8789-6297c239ab04] {\n "script": "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "dir": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "basename": "generator",\n "listing": [\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "basename": "zing.cwl",\n "size": 275\n },\n {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "basename": "pytoolgen.cwl",\n "size": 709\n }\n ]\n },\n "id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job 07d993b3-177f-45a0-8789-6297c239ab04] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator",\n "/private/tmp/docker_tmpkqg74yut/stg22aa02e0-1fa4-463f-84cf-f80e2705270f/generator",\n "Directory",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmp49cf7jpt/zing.cwl",\n "File",\n false\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmp49cf7jpt/pytoolgen.cwl",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job 07d993b3-177f-45a0-8789-6297c239ab04] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "inp.py"\n }\n]\nDEBUG cwltool:job.py:215 [job 07d993b3-177f-45a0-8789-6297c239ab04] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "/private/tmp/docker_tmp49cf7jpt/zing.cwl",\n "File",\n true\n ],\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/generator/pytoolgen.cwl",\n "/private/tmp/docker_tmp49cf7jpt/pytoolgen.cwl",\n "File",\n true\n ],\n "_:899bc3cb-ab75-4248-84a3-8ca71a12aa7b": [\n "import os\\nimport sys\\nprint(\\"\\"\\"\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n zing: string\\noutputs: {}\\narguments: [echo, $(inputs.zing)]\\n\\"\\"\\")\\n",\n "/private/tmp/docker_tmp49cf7jpt/inp.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 07d993b3-177f-45a0-8789-6297c239ab04] /private/tmp/docker_tmp49cf7jpt$ python \\\n inp.py > /private/tmp/docker_tmp49cf7jpt/main.cwl\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job 07d993b3-177f-45a0-8789-6297c239ab04] completed success\nDEBUG cwltool:job.py:422 [job 07d993b3-177f-45a0-8789-6297c239ab04] outputs {\n "runProcess": {\n "location": "file:///private/tmp/docker_tmp49cf7jpt/main.cwl",\n "basename": "main.cwl",\n "nameroot": "main",\n "nameext": ".cwl",\n "class": "File",\n "checksum": "sha1$8c160b680fb2cededef3228a53425e595b8cdf48",\n "size": 111,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job 07d993b3-177f-45a0-8789-6297c239ab04] Removing input staging directory /private/tmp/docker_tmpkqg74yut\nDEBUG cwltool:job.py:454 [job 07d993b3-177f-45a0-8789-6297c239ab04] Removing temporary directory /private/tmp/docker_tmpfwqvipwz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp49cf7jpt/main.cwl to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp49cf7jpt\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/generator/zing.cwl",\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:982 [job main.cwl_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_missing_enable_ext0/main.cwl\nDEBUG cwltool:command_line_tool.py:988 [job main.cwl_2] {\n "zing": "zipper"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job main.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job main.cwl_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(inputs.zing)"\n }\n]\nDEBUG cwltool:job.py:215 [job main.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job main.cwl_2] /private/tmp/docker_tmpofjjqo7q$ echo \\\n zipper\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job main.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job main.cwl_2] outputs {}\nDEBUG cwltool:job.py:446 [job main.cwl_2] Removing input staging directory /private/tmp/docker_tmp36cpw1ex\nDEBUG cwltool:job.py:454 [job main.cwl_2] Removing temporary directory /private/tmp/docker_tmp35m5sh1r\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpofjjqo7q\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0012447789995349012, 'start': 1685951451.6238, 'stop': 1685951451.625047, '$report_type': 'TestReport', 'item_index': 522, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_procgenerator.py::test_missing_enable_ext - location: ('tests/test_procgenerator.py', 11, 'test_missing_enable_ext') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_hello_workflow - location: ('tests/test_provenance.py', 49, 'test_hello_workflow') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_hello_workflow', 'location': ('tests/test_provenance.py', 49, 'test_hello_workflow'), 'keywords': {'test_hello_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014106010003160918, 'start': 1685951451.627031, 'stop': 1685951451.628444, '$report_type': 'TestReport', 'item_index': 523, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_not_seekable', 'location': ('tests/test_provenance.py', 684, 'test_not_seekable'), 'keywords': {'test_not_seekable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n')], 'duration': 0.008083244000772538, 'start': 1685951451.620725, 'stop': 1685951451.628809, '$report_type': 'TestReport', 'item_index': 539, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_not_seekable', 'location': ('tests/test_provenance.py', 684, 'test_not_seekable'), 'keywords': {'test_not_seekable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to 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e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt')], 'duration': 0.0024598749996584957, 'start': 1685951451.629571, 'stop': 1685951451.632032, '$report_type': 'TestReport', 'item_index': 539, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_not_seekable', 'location': ('tests/test_provenance.py', 684, 'test_not_seekable'), 'keywords': {'test_not_seekable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_seekable0/tmpjkzbyu2n')], 'duration': 0.002072841999506636, 'start': 1685951451.632972, 'stop': 1685951451.635046, '$report_type': 'TestReport', 'item_index': 539, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_not_seekable - location: ('tests/test_provenance.py', 684, 'test_not_seekable') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_not_readable - location: ('tests/test_provenance.py', 691, 'test_not_readable') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_not_readable', 'location': ('tests/test_provenance.py', 691, 'test_not_readable'), 'keywords': {'test_not_readable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s')], 'duration': 0.005643378999593551, 'start': 1685951451.636606, 'stop': 1685951451.642252, '$report_type': 'TestReport', 'item_index': 540, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_not_readable', 'location': ('tests/test_provenance.py', 691, 'test_not_readable'), 'keywords': {'test_not_readable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt')], 'duration': 0.0024552830000175163, 'start': 1685951451.642875, 'stop': 1685951451.645331, '$report_type': 'TestReport', 'item_index': 540, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_not_readable', 'location': ('tests/test_provenance.py', 691, 'test_not_readable'), 'keywords': {'test_not_readable': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/file.txt.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha256.txt: 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Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e file.txt'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_not_readable0/tmpyvxrpn6s\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary 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'test_truncate_fails') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_truncate_fails', 'location': ('tests/test_provenance.py', 698, 'test_truncate_fails'), 'keywords': {'test_truncate_fails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw3] received command runtests {'indices': [543, 544, 545, 546, 547]}\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33\x1b[0m\n"), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: 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cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha1.txt: 726c76553e1a3fdea29134f36e6af2ea05ec5cce file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha256.txt: 4e47826698bb4630fb4451010062fadbf85d61427cbdfaed7ad0f23f239bed89 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha512.txt: 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\x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha1.txt: 726c76553e1a3fdea29134f36e6af2ea05ec5cce file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha256.txt: 4e47826698bb4630fb4451010062fadbf85d61427cbdfaed7ad0f23f239bed89 file.txt\n\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha512.txt: 567683ddba1f5a576b68ec26f41ffbcc7e718d646839ac6c2ef746fe952cef4cbe6dea635bc2f098b92b65caacf482333bb9d1d9a3089bc4f01cb86f7a2fbc18 file.txt\n\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/file.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha1.txt: 726c76553e1a3fdea29134f36e6af2ea05ec5cce file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha256.txt: 4e47826698bb4630fb4451010062fadbf85d61427cbdfaed7ad0f23f239bed89 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_truncate_fails0/tmp8r5k2a33/tagmanifest-sha512.txt: 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<_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_truncate_fails - location: ('tests/test_provenance.py', 698, 'test_truncate_fails') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-0097-True] - location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-0097-True]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_check_mod_11_2[0000-0002-1825-0097-True]', 'location': ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1825-0097-True]'), 'keywords': {'test_check_mod_11_2[0000-0002-1825-0097-True]': 1, 'parametrize': 1, 'pytestmark': 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'keywords': {'test_check_mod_11_2[0000-0002-1825-0097-True]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-0097-True': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00038638800015178276, 'start': 1685951451.666068, 'stop': 1685951451.666456, '$report_type': 'TestReport', 'item_index': 542, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 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script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp44oq2voa\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp44oq2voa\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7918996069993227, 'start': 1685951450.9114509, 'stop': 1685951451.7033339, '$report_type': 'TestReport', 'item_index': 506, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_runtest_logreport --> [] [hook] - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_check_mod_11_2[0000-0002-1694-2330-False] - location: ('tests/test_provenance.py', 726, 'test_check_mod_11_2[0000-0002-1694-2330-False]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011373939996701665, 'start': 1685951451.705606, 'stop': 1685951451.706746, '$report_type': 'TestReport', 'item_index': 552, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]'), 'keywords': {'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "график",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test"\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test",\n "dirname": "/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp44oq2voa\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/script",\n "input": {\n "class": 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"/private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmp44oq2voa$ cat \\\n /private/tmp/docker_tmpdb7gxqh8/stg557fa812-30aa-465f-86a9-c0700461c9fe/test > /private/tmp/docker_tmp44oq2voa/график\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp44oq2voa/%D0%B3%D1%80%D0%B0%D1%84%D0%B8%D0%BA",\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpdb7gxqh8\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp77pek0_e\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp44oq2voa/график to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__1/outdir/график\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp44oq2voa\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0011550549997991766, 'start': 1685951451.705198, 'stop': 1685951451.7063549, '$report_type': 'TestReport', 'item_index': 506, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0433\u0440\u0430\u0444\u0438\u043a] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0014078220001465525, 'start': 1685951451.707592, 'stop': 1685951451.709002, '$report_type': 'TestReport', 'item_index': 552, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003332229998704861, 'start': 1685951451.7095811, 'stop': 1685951451.7099159, '$report_type': 'TestReport', 'item_index': 552, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]'), 'keywords': {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0022639859998889733, 'start': 1685951451.709167, 'stop': 1685951451.711433, '$report_type': 'TestReport', 'item_index': 507, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 745, 'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]') - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007346430002144189, 'start': 1685951451.711381, 'stop': 1685951451.712117, '$report_type': 'TestReport', 'item_index': 553, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003641949997472693, 'start': 1685951451.712659, 'stop': 1685951451.713024, '$report_type': 'TestReport', 'item_index': 553, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002946350005004206, 'start': 1685951451.713682, 'stop': 1685951451.713978, '$report_type': 'TestReport', 'item_index': 553, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 745, 'test_valid_orcid[http://orcid.org/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097] - location: ('tests/test_provenance.py', 745, 'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]'), 'keywords': {'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00045533299999078736, 'start': 1685951451.714863, 'stop': 1685951451.7153192, '$report_type': 'TestReport', 'item_index': 554, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] -433\\u0440\\u0430\\u0444\\u0438\\u043a"\n}\nDEBUG pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]'), 'keywords': {'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00032317899967893027, 'start': 1685951451.716031, 'stop': 1685951451.716356, '$report_type': 'TestReport', 'item_index': 554, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]'), 'keywords': {'test_valid_orcid[0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1825-0097-https://orcid.org/0000-0002-1825-0097': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 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'test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', "[worker-gw3] received command runtests {'indices': [557, 558, 559, 560]}\n")], 'duration': 0.00044140499994682614, 'start': 1685951451.719826, 'stop': 1685951451.720269, '$report_type': 'TestReport', 'item_index': 555, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - 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'duration': 0.00029204699967522174, 'start': 1685951451.720681, 'stop': 1685951451.7209752, '$report_type': 'TestReport', 'item_index': 555, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 745, 'test_valid_orcid[https://orcid.org/0000-0002-1694-233x-https://orcid.org/0000-0002-1694-233X]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: 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{'test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005485689998749876, 'start': 1685951451.72414, 'stop': 1685951451.724691, '$report_type': 'TestReport', 'item_index': 556, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 745, 'test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_valid_orcid[https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://ORCID.ORG/0000-0002-1694-233X-https://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00041454499933024636, 'start': 1685951451.7256389, 'stop': 1685951451.726055, '$report_type': 'TestReport', 'item_index': 556, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - 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'tests/test_provenance.py::test_invalid_orcid[0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[0002-1694-2332]'), 'keywords': {'test_invalid_orcid[0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, '0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00039211800049088197, 'start': 1685951451.7279549, 'stop': 1685951451.728348, '$report_type': 'TestReport', 'item_index': 557, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: 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'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00043069900038972264, 'start': 1685951451.730485, 'stop': 1685951451.7309172, '$report_type': 'TestReport', 'item_index': 558, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]'), 'keywords': {'test_invalid_orcid[https://orcid.org/0000-0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/0000-0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002679489998627105, 'start': 1685951451.731301, 'stop': 1685951451.73157, '$report_type': 'TestReport', 'item_index': 558, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 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'item_index': 559, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[0000-0002-1694-2332] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[0000-0002-1694-2332]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[0000-0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[0000-0002-1694-2332]'), 'keywords': {'test_invalid_orcid[0000-0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0005299230006130529, 'start': 1685951451.73413, 'stop': 1685951451.734661, '$report_type': 'TestReport', 'item_index': 559, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[0000-0002-1694-2332]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[0000-0002-1694-2332]'), 'keywords': {'test_invalid_orcid[0000-0002-1694-2332]': 1, 'parametrize': 1, 'pytestmark': 1, '0000-0002-1694-2332': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002615349994812277, 'start': 1685951451.735347, 'stop': 1685951451.735609, '$report_type': 'TestReport', 'item_index': 559, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[0000-0002-1694-2332] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[0000-0002-1694-2332]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[https://orcid.org/000000021694233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/000000021694233X]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org/000000021694233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/000000021694233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org/000000021694233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/000000021694233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003034880000996054, 'start': 1685951451.7363992, 'stop': 1685951451.736703, '$report_type': 'TestReport', 'item_index': 560, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org/000000021694233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/000000021694233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org/000000021694233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/000000021694233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00024056900019786553, 'start': 1685951451.73705, 'stop': 1685951451.737292, '$report_type': 'TestReport', 'item_index': 560, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org/000000021694233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/000000021694233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org/000000021694233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org/000000021694233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002578959993115859, 'start': 1685951451.737841, 'stop': 1685951451.7381, '$report_type': 'TestReport', 'item_index': 560, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[https://orcid.org/000000021694233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org/000000021694233X]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[000000021694233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[000000021694233X]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[000000021694233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[000000021694233X]'), 'keywords': {'test_invalid_orcid[000000021694233X]': 1, 'parametrize': 1, 'pytestmark': 1, '000000021694233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005018640003982, 'start': 1685951451.7391071, 'stop': 1685951451.739611, '$report_type': 'TestReport', 'item_index': 561, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish 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'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[000000021694233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[000000021694233X]'), 'keywords': {'test_invalid_orcid[000000021694233X]': 1, 'parametrize': 1, 'pytestmark': 1, '000000021694233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00046694299999217037, 'start': 1685951451.7413929, 'stop': 1685951451.7418618, '$report_type': 'TestReport', 'item_index': 561, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[000000021694233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[000000021694233X]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[https://example.org/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://example.org/0000-0002-1694-233X]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://example.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://example.org/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[https://example.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://example.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004732390007120557, 'start': 1685951451.743167, 'stop': 1685951451.7436411, '$report_type': 'TestReport', 'item_index': 562, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: 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finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://example.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://example.org/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[https://example.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://example.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00025080300019908464, 'start': 1685951451.7451782, 'stop': 1685951451.74543, '$report_type': 'TestReport', 'item_index': 562, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[https://example.org/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://example.org/0000-0002-1694-233X]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'ftp://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002909930008172523, 'start': 1685951451.7472482, 'stop': 1685951451.74754, '$report_type': 'TestReport', 'item_index': 563, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'ftp://orcid.org/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004054629998790915, 'start': 1685951451.748232, 'stop': 1685951451.748638, '$report_type': 'TestReport', 'item_index': 563, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[ftp://orcid.org/0000-0002-1694-233X]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org:443/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00045285899977898225, 'start': 1685951451.7498848, 'stop': 1685951451.750339, '$report_type': 'TestReport', 'item_index': 564, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org:443/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002515780006433488, 'start': 1685951451.750687, 'stop': 1685951451.750939, '$report_type': 'TestReport', 'item_index': 564, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] -[hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_normalizeFilesDirs[file-file_dir1-expected1]', 'location': ('tests/test_pathmapper.py', 66, 'test_normalizeFilesDirs[file-file_dir1-expected1]'), 'keywords': {'test_normalizeFilesDirs[file-file_dir1-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, 'file-file_dir1-expected1': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0004152450001129182, 'start': 1685951448.650466, 'stop': 1685951448.650882, '$report_type': 'TestReport', 'item_index': 514, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'https://orcid.org:443/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003813679995801067, 'start': 1685951451.751585, 'stop': 1685951451.751968, '$report_type': 'TestReport', 'item_index': 564, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[https://orcid.org:443/0000-0002-1694-233X]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org:80/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0004132009999011643, 'start': 1685951451.752942, 'stop': 1685951451.7533572, '$report_type': 'TestReport', 'item_index': 565, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org:80/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0006339709998428589, 'start': 1685951451.753885, 'stop': 1685951451.7545211, '$report_type': 'TestReport', 'item_index': 565, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]'), 'keywords': {'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]': 1, 'parametrize': 1, 'pytestmark': 1, 'http://orcid.org:80/0000-0002-1694-233X': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003594289992179256, 'start': 1685951451.7551591, 'stop': 1685951451.75552, '$report_type': 'TestReport', 'item_index': 565, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[http://orcid.org:80/0000-0002-1694-233X]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[]'), 'keywords': {'test_invalid_orcid[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006703340004605707, 'start': 1685951451.757062, 'stop': 1685951451.757735, '$report_type': 'TestReport', 'item_index': 566, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[]'), 'keywords': {'test_invalid_orcid[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003938019999623066, 'start': 1685951451.758364, 'stop': 1685951451.75876, '$report_type': 'TestReport', 'item_index': 566, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_invalid_orcid[]', 'location': ('tests/test_provenance.py', 771, 'test_invalid_orcid[]'), 'keywords': {'test_invalid_orcid[]': 1, 'parametrize': 1, 'pytestmark': 1, '': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003428029995120596, 'start': 1685951451.759594, 'stop': 1685951451.759939, '$report_type': 'TestReport', 'item_index': 566, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_invalid_orcid[] - location: ('tests/test_provenance.py', 771, 'test_invalid_orcid[]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_whoami - location: ('tests/test_provenance.py', 777, 'test_whoami') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_whoami', 'location': ('tests/test_provenance.py', 777, 'test_whoami'), 'keywords': {'test_whoami': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002886559996113647, 'start': 1685951451.760962, 'stop': 1685951451.7612522, '$report_type': 'TestReport', 'item_index': 567, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_whoami', 'location': ('tests/test_provenance.py', 777, 'test_whoami'), 'keywords': {'test_whoami': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0029586099999505677, 'start': 1685951451.761823, 'stop': 1685951451.7647831, '$report_type': 'TestReport', 'item_index': 567, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_whoami', 'location': ('tests/test_provenance.py', 777, 'test_whoami'), 'keywords': {'test_whoami': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00024329300049430458, 'start': 1685951451.765263, 'stop': 1685951451.7655082, '$report_type': 'TestReport', 'item_index': 567, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_whoami - location: ('tests/test_provenance.py', 777, 'test_whoami') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_research_object - location: ('tests/test_provenance.py', 783, 'test_research_object') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_research_object', 'location': ('tests/test_provenance.py', 783, 'test_research_object'), 'keywords': {'test_research_object': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00024808000034681754, 'start': 1685951451.7682009, 'stop': 1685951451.768451, '$report_type': 'TestReport', 'item_index': 568, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_research_object', 'location': ('tests/test_provenance.py', 783, 'test_research_object'), 'keywords': {'test_research_object': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00037334899934649, 'start': 1685951451.7691488, 'stop': 1685951451.7695239, '$report_type': 'TestReport', 'item_index': 568, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_research_object', 'location': ('tests/test_provenance.py', 783, 'test_research_object'), 'keywords': {'test_research_object': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00030079200041654985, 'start': 1685951451.770102, 'stop': 1685951451.770405, '$report_type': 'TestReport', 'item_index': 568, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_research_object - location: ('tests/test_provenance.py', 783, 'test_research_object') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_research_object_picklability - location: ('tests/test_provenance.py', 788, 'test_research_object_picklability') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_research_object_picklability', 'location': ('tests/test_provenance.py', 788, 'test_research_object_picklability'), 'keywords': {'test_research_object_picklability': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj')], 'duration': 0.023298113999771886, 'start': 1685951451.772306, 'stop': 1685951451.795605, '$report_type': 'TestReport', 'item_index': 569, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_research_object_picklability', 'location': ('tests/test_provenance.py', 788, 'test_research_object_picklability'), 'keywords': {'test_research_object_picklability': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj')], 'duration': 0.0006209909997778595, 'start': 1685951451.796177, 'stop': 1685951451.796799, '$report_type': 'TestReport', 'item_index': 569, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_research_object_picklability', 'location': ('tests/test_provenance.py', 788, 'test_research_object_picklability'), 'keywords': {'test_research_object_picklability': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj\x1b[0m\n'), ('Captured log teardown', 'DEBUG cwltool:writablebagfile.py:213 [provenance] Deleting temporary /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_research_object_picklabil0/tmp4m0qt_uj')], 'duration': 0.00234540899964486, 'start': 1685951451.797377, 'stop': 1685951451.799724, '$report_type': 'TestReport', 'item_index': 569, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_research_object_picklability - location: ('tests/test_provenance.py', 788, 'test_research_object_picklability') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_directory_workflow_no_listing - location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow_no_listing', 'location': ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing'), 'keywords': {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016229729999395204, 'start': 1685951451.801435, 'stop': 1685951451.80306, '$report_type': 'TestReport', 'item_index': 570, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]'), 'keywords': {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/%F0%92%81%83",\n "basename": "ð’ƒ",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmppaqyosg7\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppaqyosg7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7048519689997192, 'start': 1685951451.7120519, 'stop': 1685951452.416888, '$report_type': 'TestReport', 'item_index': 507, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]'), 'keywords': {'test_unicode_in_output_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/%F0%92%81%83",\n "basename": "ð’ƒ",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmppaqyosg7\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test"\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\ud808\\udc43"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test",\n "dirname": "/private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmppaqyosg7$ cat \\\n /private/tmp/docker_tmpyq30h8uv/stgf4bc1bd3-4cd0-4822-a928-da53d1f3e217/test > /private/tmp/docker_tmppaqyosg7/ð’ƒ\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmppaqyosg7/%F0%92%81%83",\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmpyq30h8uv\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmphq941b4k\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmppaqyosg7/ð’ƒ to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__2/outdir/ð’ƒ\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmppaqyosg7\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006576920004590647, 'start': 1685951452.418154, 'stop': 1685951452.418813, '$report_type': 'TestReport', 'item_index': 507, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\U00012043] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\U00012043]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0023664050004299497, 'start': 1685951452.4210129, 'stop': 1685951452.423381, '$report_type': 'TestReport', 'item_index': 508, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_parallel.py::test_sequential_workflow', 'location': ('tests/test_parallel.py', 10, 'test_sequential_workflow'), 'keywords': {'test_sequential_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] inputs {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] start\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] starting step step1_3\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1_3\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_3), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1_3] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1,target=/GbFKKR \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/5jjsgruc/20230605095051-246049.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt > /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] Max memory used: 0MiB\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] outputs {\n "output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] Removing input staging directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/hklbq548\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] Removing temporary directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] starting step step2_3\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step2_3] start\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step2_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] outputs {\n "count_output": 16\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fqocvrn2\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _5] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _5] inputs {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:610 [workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\nINFO cwltool:workflow_job.py:765 [workflow _5] start\nINFO cwltool:workflow_job.py:613 [workflow _5] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_3), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:610 [workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1_3] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1_3] /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1,target=/GbFKKR \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/5jjsgruc/20230605095051-246049.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt > /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output\nINFO cwltool:job.py:905 [job step1_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/hklbq548\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb\nINFO cwltool:workflow_job.py:613 [workflow _5] starting step step2_3\nDEBUG cwltool:workflow_job.py:727 [step step2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_3] start\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:564 [step step2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _5] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fqocvrn2')], 'duration': 1.3139026039998498, 'start': 1685951451.118825, 'stop': 1685951452.432698, '$report_type': 'TestReport', 'item_index': 494, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_parallel.py::test_sequential_workflow', 'location': ('tests/test_parallel.py', 10, 'test_sequential_workflow'), 'keywords': {'test_sequential_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] inputs {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] start\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] starting step step1_3\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1_3\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_3), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m[job step1_3] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\x1b[0m\n\x1b[32m[2023-06-05 09:50:51]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1,target=/GbFKKR \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/5jjsgruc/20230605095051-246049.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt > /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] Max memory used: 0MiB\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] outputs {\n "output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] Removing input staging directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/hklbq548\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_3] Removing temporary directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] starting step step2_3\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step2_3] start\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step2_3] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _5] completed success\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _5] outputs {\n "count_output": 16\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1\x1b[0m\n\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fqocvrn2\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _5] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl\nDEBUG cwltool:workflow_job.py:777 [workflow _5] inputs {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:610 [workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\nINFO cwltool:workflow_job.py:765 [workflow _5] start\nINFO cwltool:workflow_job.py:613 [workflow _5] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/wc-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "location": "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "size": 1111\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_3), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:610 [workflow _5] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2 not ready\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nWARNING cwltool:docker.py:423 [job step1_3] Skipping Docker software container \'--memory\' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.\nINFO cwltool:job.py:266 [job step1_3] /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1,target=/GbFKKR \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt,readonly \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/5jjsgruc/20230605095051-246049.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg6675884d-fc65-46f8-bcc1-c7545b258592/whale.txt > /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output\nINFO cwltool:job.py:905 [job step1_3] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step1/output": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/hklbq548\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/c6ig0bbb\nINFO cwltool:workflow_job.py:613 [workflow _5] starting step step2_3\nDEBUG cwltool:workflow_job.py:727 [step step2_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step2_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/file1": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:75 [step step2_3] start\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:workflow_job.py:564 [step step2_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/count-lines1-wf.cwl#step2/output": 16\n}\nINFO cwltool:workflow_job.py:572 [step step2_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _5] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _5] outputs {\n "count_output": 16\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h6t3nie1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/fqocvrn2')], 'duration': 0.000757715999498032, 'start': 1685951452.434391, 'stop': 1685951452.4351501, '$report_type': 'TestReport', 'item_index': 494, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_parallel.py::test_sequential_workflow - location: ('tests/test_parallel.py', 10, 'test_sequential_workflow') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_parallel.py::test_scattered_workflow', 'location': ('tests/test_parallel.py', 23, 'test_scattered_workflow'), 'keywords': {'test_scattered_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002563279995229095, 'start': 1685951452.436842, 'stop': 1685951452.437099, '$report_type': 'TestReport', 'item_index': 495, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_parallel.py::test_scattered_workflow - location: ('tests/test_parallel.py', 23, 'test_scattered_workflow') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_hello_workflow', 'location': ('tests/test_provenance.py', 49, 'test_hello_workflow'), 'keywords': {'test_hello_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "response": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt",\n "basename": "response.txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl --usermessage Hello workflow\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpglr7rc0q/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step0_4\n\x1b[1;30mINFO\x1b[0m [step step0_4] start\n\x1b[1;30mINFO\x1b[0m [job step0_4] /private/tmp/docker_tmpky30xwh8$ echo \\\n -n \\\n -e \\\n 'Hello workflow' > /private/tmp/docker_tmpky30xwh8/response.txt\n\x1b[1;30mINFO\x1b[0m [job step0_4] completed success\n\x1b[1;30mINFO\x1b[0m [step step0_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl --usermessage Hello workflow\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\', job_order=[\'--usermessage\', \'Hello workflow\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 327fe927e223c88dca78a0ea5105c922f0fba00b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 60f0e978a2ac9c4ef469177fbe58189c76d2dd6b39c5c6b660c5ecb3ccd3d2a4 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: ab665a7342ac208014e8bcb016f5643a0cbc1cc5f45595616f992dbd30e3b98324bca187d0fec8ef4f5a9de604932b3caf0fe61771af4baeea9a3d946ae2fefd workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpglr7rc0q/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl",\n "usermessage": "Hello workflow"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'usermessage\': \'Hello workflow\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello workflow\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: d4facb14439b8696b380c65f8efc92e00bffbfa2 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: cea82f27619ef873390bbd420bc76eaf38ff6428f3bdc3e0decb7b915885e1ce workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: feab70d27d2c04c33d6fad2eebf6476963a889161fb4664d48aeeacbc1954d14c73d1be159b8b14bb5bee6568ea24a2a34eaa5442216bfbafdac08304a6e43e3 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/manifest-sha1.txt: 260807aefd9032a48a0d88d4ff7110a5bbfaea3d data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "usermessage": "Hello workflow"\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step0_4\nDEBUG cwltool:workflow_job.py:727 [step step0_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/message": "Hello workflow"\n}\nDEBUG cwltool:workflow_job.py:732 [step step0_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/message": "Hello workflow"\n}\nINFO cwltool:workflow_job.py:75 [step step0_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step0_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/78eec50f-a8c4-49ef-b819-b3549af9288a as part of step step0_4\nDEBUG cwltool:command_line_tool.py:988 [job step0_4] {\n "message": "Hello workflow"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step0_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step0_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-e"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello workflow"\n }\n]\nDEBUG cwltool:job.py:215 [job step0_4] initial work dir {}\nINFO cwltool:job.py:266 [job step0_4] /private/tmp/docker_tmpky30xwh8$ echo \\\n -n \\\n -e \\\n \'Hello workflow\' > /private/tmp/docker_tmpky30xwh8/response.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/manifest-sha1.txt: ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nINFO cwltool:job.py:419 [job step0_4] completed success\nDEBUG cwltool:job.py:422 [job step0_4] outputs {\n "response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step0_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nINFO cwltool:workflow_job.py:572 [step step0_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nDEBUG cwltool:job.py:446 [job step0_4] Removing input staging directory /private/tmp/docker_tmphlf_rba8\nDEBUG cwltool:job.py:454 [job step0_4] Removing temporary directory /private/tmp/docker_tmp7h1158q7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpky30xwh8/response.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfkeo19kl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpky30xwh8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: efb0801b16087469a4510229b16bfcff66750932 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 2230d4ebababf075d8fbc7e04f19411178b0b594711eff698a6da6084e19f480 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 1a3847b8bc1ae8ffecfc640d7a473975d5b1e216830043bd6a98aec214ddd9a4b01e979fa7111dbd4936aa1390a0498e6e9169b965317424d4e70a4d63f45e6a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 9b771bb6461f656650a1bfb6000ea190b1bddd35 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: d41f4929fa8d97fafc3b2034e3bbd869bc05803a137b70afa382c8e3661646dc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: aa49365eaeb9437311c0aa2b912741047a21ba9c44f7e0ef7c88c0c700921ff4c909e7655ebb793b0b83d9a546058b7cb7647867c69e372b1d41bb6290fef3f8 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 90441e825ca65d0df8ce3b48c504a2e973bceef9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: f0e7a69d8bc9bfac7979e0e9acbf945b4e8e5d0056d02a0f25e0d693fdd57488 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: a0f1727b0560d4bf9ec294531561cef5775ebee76ee71de7fff3027a47170c9992538c9a00853663ace4ade59bbc09886a7018c62a9f9436753d460a28ffd98b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 9a0f27052dd2175caf2a67758f7691746e41ccd2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 1a8c28680fbb8bac16231a866740bbaeb15581e14a9377ff970b5e85c89999fc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: e65b6e2a1abcb2d07d64e5680662c38a4bffc93ed129a4c704e53229ffbed61895d5687b6ac94d786616db330f1afbd3782c8574812633500833f9607b210d25 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 1ad236bd4b38764eda7811f98521099ffb363ecc metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 0c6df5b09f2c2a7e8f9608a5764566395bad043ca95ca93a6cedf92f2c799e0e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 969f2cf9ed709f655ee14e64530bc5fb2b09a6658bc66ad71b0656f870b55eb702e2a9f5a5583174fdb9a9d4d20e8f7125b35c731dd63ff39b8878de2b0023cf metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 189f0652a59dbaa89976f6b3f9d8257ef9d098ea metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 518d054df5fb1de9a011e6bff56ac8a1bef2feab49691f4db926372c49019f7a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 21f81b0d457e735d55dce20c5388f10ec251bf2e228ffbee2c4ac221c6449998f0adef0ce764361381d4ac73ad9907b4eeaf32d82426c254c4c9a579b5fbd3aa metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'response\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\', \'basename\': \'response.txt\', \'nameroot\': \'response\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\', \'size\': 17, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\', \'basename\': \'response.txt\', \'nameroot\': \'response\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\', \'size\': 17, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: response.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: response\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 17\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 618f86915ea9700ecb3b704795a4ae85bf643425 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 8ac22a6c1cabae7deb3b29b0e2bda23e71052570143f0acbf2a09da703487dca workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: cf6d7a5f6330db6c0e0852718916891cc1444442f31cd4cfbba37b618d91f92004d2596775718de660ae2532c587e013c37ed7e795796cdc8ed34d0899661322 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: e1fc01826e8384fb32a1064690707df6334017bb snapshot/hello-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 01d934f8701a6367ebb2d2e1ec8834d6da95f348521dba8612633e4be6252965 snapshot/hello-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: d75bcdacf77bb436846d87bf6cbb243d7720a2bc1b3b165e6558df9a82ebdde0baea7a5ae91afebd85fc3e0ad3165f1523ea73a409b46f86ee6c7385a6b647d3 snapshot/hello-workflow.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 555f09620cd5b296ed8407059a0f2357ea0bb092 metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: ac58b85e9b87b81165c5fc2f3739964d2666cefada2b344661084a7e5218341e metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 001951b3906ae97db9f6bd8dec485bb4563f70697ed163e0521bdec155d0b7e9223019c1a0525300708ee55653cba9a80c2e0edae23fff7bbac807811bbbc236 metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 8d7b3a5c56948366a29ee377680d0ac38129de05 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 23801bfbbba411f431e6b84bf181dc5514967c8e824f82728e70a2fda8be11ce metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 2671f6b2e92069ea01f98c638d4e5eb042aee0b59619147d2925f3603a504581fc874f715a039897175a5f63b3f1acb6f662a0ab488a4e000b797c5ea53a6d45 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 5f3f3974d5347536a098f33eb55826382755b5a8 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 05b4f6a002ef3f090d70b6ade829ca1bf679eac0abe89707ca5ccf3d6d74b193 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: b424ef8f2d9859451976287a408004919705b84b3bc642e1e877560d117acefdd7ea5431438decfcb8e3bc24c5d758156005b869df64c4dfffefa29e9559c60a bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance')], 'duration': 1.1406687319995399, 'start': 1685951451.628845, 'stop': 1685951452.7694871, '$report_type': 'TestReport', 'item_index': 523, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_hello_workflow', 'location': ('tests/test_provenance.py', 49, 'test_hello_workflow'), 'keywords': {'test_hello_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "response": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt",\n "basename": "response.txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl --usermessage Hello workflow\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpglr7rc0q/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step0_4\n\x1b[1;30mINFO\x1b[0m [step step0_4] start\n\x1b[1;30mINFO\x1b[0m [job step0_4] /private/tmp/docker_tmpky30xwh8$ echo \\\n -n \\\n -e \\\n 'Hello workflow' > /private/tmp/docker_tmpky30xwh8/response.txt\n\x1b[1;30mINFO\x1b[0m [job step0_4] completed success\n\x1b[1;30mINFO\x1b[0m [step step0_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl --usermessage Hello workflow\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\', job_order=[\'--usermessage\', \'Hello workflow\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 327fe927e223c88dca78a0ea5105c922f0fba00b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 60f0e978a2ac9c4ef469177fbe58189c76d2dd6b39c5c6b660c5ecb3ccd3d2a4 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: ab665a7342ac208014e8bcb016f5643a0cbc1cc5f45595616f992dbd30e3b98324bca187d0fec8ef4f5a9de604932b3caf0fe61771af4baeea9a3d946ae2fefd workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpglr7rc0q/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl",\n "usermessage": "Hello workflow"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'usermessage\': \'Hello workflow\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello workflow\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: d4facb14439b8696b380c65f8efc92e00bffbfa2 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: cea82f27619ef873390bbd420bc76eaf38ff6428f3bdc3e0decb7b915885e1ce workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: feab70d27d2c04c33d6fad2eebf6476963a889161fb4664d48aeeacbc1954d14c73d1be159b8b14bb5bee6568ea24a2a34eaa5442216bfbafdac08304a6e43e3 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/manifest-sha1.txt: 260807aefd9032a48a0d88d4ff7110a5bbfaea3d data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "usermessage": "Hello workflow"\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step0_4\nDEBUG cwltool:workflow_job.py:727 [step step0_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/message": "Hello workflow"\n}\nDEBUG cwltool:workflow_job.py:732 [step step0_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/message": "Hello workflow"\n}\nINFO cwltool:workflow_job.py:75 [step step0_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step0_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/78eec50f-a8c4-49ef-b819-b3549af9288a as part of step step0_4\nDEBUG cwltool:command_line_tool.py:988 [job step0_4] {\n "message": "Hello workflow"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step0_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step0_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-e"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello workflow"\n }\n]\nDEBUG cwltool:job.py:215 [job step0_4] initial work dir {}\nINFO cwltool:job.py:266 [job step0_4] /private/tmp/docker_tmpky30xwh8$ echo \\\n -n \\\n -e \\\n \'Hello workflow\' > /private/tmp/docker_tmpky30xwh8/response.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/26/260807aefd9032a48a0d88d4ff7110a5bbfaea3d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/manifest-sha1.txt: ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nINFO cwltool:job.py:419 [job step0_4] completed success\nDEBUG cwltool:job.py:422 [job step0_4] outputs {\n "response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step0_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/hello-workflow.cwl#step0/response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nINFO cwltool:workflow_job.py:572 [step step0_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "response": {\n "location": "file:///private/tmp/docker_tmpky30xwh8/response.txt",\n "basename": "response.txt",\n "nameroot": "response",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e",\n "size": 17,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f"\n }\n}\nDEBUG cwltool:job.py:446 [job step0_4] Removing input staging directory /private/tmp/docker_tmphlf_rba8\nDEBUG cwltool:job.py:454 [job step0_4] Removing temporary directory /private/tmp/docker_tmp7h1158q7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpky30xwh8/response.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfkeo19kl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpky30xwh8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: efb0801b16087469a4510229b16bfcff66750932 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 2230d4ebababf075d8fbc7e04f19411178b0b594711eff698a6da6084e19f480 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 1a3847b8bc1ae8ffecfc640d7a473975d5b1e216830043bd6a98aec214ddd9a4b01e979fa7111dbd4936aa1390a0498e6e9169b965317424d4e70a4d63f45e6a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 9b771bb6461f656650a1bfb6000ea190b1bddd35 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: d41f4929fa8d97fafc3b2034e3bbd869bc05803a137b70afa382c8e3661646dc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: aa49365eaeb9437311c0aa2b912741047a21ba9c44f7e0ef7c88c0c700921ff4c909e7655ebb793b0b83d9a546058b7cb7647867c69e372b1d41bb6290fef3f8 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 90441e825ca65d0df8ce3b48c504a2e973bceef9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: f0e7a69d8bc9bfac7979e0e9acbf945b4e8e5d0056d02a0f25e0d693fdd57488 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: a0f1727b0560d4bf9ec294531561cef5775ebee76ee71de7fff3027a47170c9992538c9a00853663ace4ade59bbc09886a7018c62a9f9436753d460a28ffd98b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 9a0f27052dd2175caf2a67758f7691746e41ccd2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 1a8c28680fbb8bac16231a866740bbaeb15581e14a9377ff970b5e85c89999fc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: e65b6e2a1abcb2d07d64e5680662c38a4bffc93ed129a4c704e53229ffbed61895d5687b6ac94d786616db330f1afbd3782c8574812633500833f9607b210d25 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 1ad236bd4b38764eda7811f98521099ffb363ecc metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 0c6df5b09f2c2a7e8f9608a5764566395bad043ca95ca93a6cedf92f2c799e0e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 969f2cf9ed709f655ee14e64530bc5fb2b09a6658bc66ad71b0656f870b55eb702e2a9f5a5583174fdb9a9d4d20e8f7125b35c731dd63ff39b8878de2b0023cf metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 189f0652a59dbaa89976f6b3f9d8257ef9d098ea metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 518d054df5fb1de9a011e6bff56ac8a1bef2feab49691f4db926372c49019f7a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 21f81b0d457e735d55dce20c5388f10ec251bf2e228ffbee2c4ac221c6449998f0adef0ce764361381d4ac73ad9907b4eeaf32d82426c254c4c9a579b5fbd3aa metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'response\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\', \'basename\': \'response.txt\', \'nameroot\': \'response\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\', \'size\': 17, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/cwltool-run/response.txt\', \'basename\': \'response.txt\', \'nameroot\': \'response\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\', \'size\': 17, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/ff/ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: response.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: response\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$ff1f8b01ee9e74ec5f9840aa07ea6bc2895a235e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 17\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:aa651cac-e6da-4d31-9842-8833f7ed560f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 618f86915ea9700ecb3b704795a4ae85bf643425 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 8ac22a6c1cabae7deb3b29b0e2bda23e71052570143f0acbf2a09da703487dca workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: cf6d7a5f6330db6c0e0852718916891cc1444442f31cd4cfbba37b618d91f92004d2596775718de660ae2532c587e013c37ed7e795796cdc8ed34d0899661322 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: e1fc01826e8384fb32a1064690707df6334017bb snapshot/hello-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 01d934f8701a6367ebb2d2e1ec8834d6da95f348521dba8612633e4be6252965 snapshot/hello-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: d75bcdacf77bb436846d87bf6cbb243d7720a2bc1b3b165e6558df9a82ebdde0baea7a5ae91afebd85fc3e0ad3165f1523ea73a409b46f86ee6c7385a6b647d3 snapshot/hello-workflow.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 555f09620cd5b296ed8407059a0f2357ea0bb092 metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: ac58b85e9b87b81165c5fc2f3739964d2666cefada2b344661084a7e5218341e metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 001951b3906ae97db9f6bd8dec485bb4563f70697ed163e0521bdec155d0b7e9223019c1a0525300708ee55653cba9a80c2e0edae23fff7bbac807811bbbc236 metadata/logs/engine.560106f6-35e5-4d68-afe8-30137aea5b76.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 8d7b3a5c56948366a29ee377680d0ac38129de05 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 23801bfbbba411f431e6b84bf181dc5514967c8e824f82728e70a2fda8be11ce metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: 2671f6b2e92069ea01f98c638d4e5eb042aee0b59619147d2925f3603a504581fc874f715a039897175a5f63b3f1acb6f662a0ab488a4e000b797c5ea53a6d45 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha1.txt: 5f3f3974d5347536a098f33eb55826382755b5a8 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha256.txt: 05b4f6a002ef3f090d70b6ade829ca1bf679eac0abe89707ca5ccf3d6d74b193 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax/tagmanifest-sha512.txt: b424ef8f2d9859451976287a408004919705b84b3bc642e1e877560d117acefdd7ea5431438decfcb8e3bc24c5d758156005b869df64c4dfffefa29e9559c60a bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/yjl8a8ax\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_workflow0/provenance')], 'duration': 0.001052595000146539, 'start': 1685951452.7712488, 'stop': 1685951452.7723038, '$report_type': 'TestReport', 'item_index': 523, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_hello_workflow - location: ('tests/test_provenance.py', 49, 'test_hello_workflow') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - when: runtest - nodeid: tests/test_provenance.py::test_hello_workflow - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_hello_single_tool - location: ('tests/test_provenance.py', 61, 'test_hello_single_tool') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_hello_single_tool', 'location': ('tests/test_provenance.py', 61, 'test_hello_single_tool'), 'keywords': {'test_hello_single_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011711050001395051, 'start': 1685951452.7750342, 'stop': 1685951452.7762072, '$report_type': 'TestReport', 'item_index': 524, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl'")], 'duration': 5.263246608000372, 'start': 1685951447.551656, 'stop': 1685951452.814772, '$report_type': 'TestReport', 'item_index': 484, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]', 'location': ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]'), 'keywords': {'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]': 1, 'parametrize': 1, 'pytestmark': 1, 'tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:47]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort_datetime.cwl'")], 'duration': 0.0003758709999601706, 'start': 1685951452.815354, 'stop': 1685951452.815731, '$report_type': 'TestReport', 'item_index': 484, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl] - location: ('tests/test_pack.py', 23, 'test_packing[tests/wf/revsort_datetime.cwl-tests/wf/expect_revsort_datetime_packed.cwl]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_pack_single_tool - location: ('tests/test_pack.py', 67, 'test_pack_single_tool') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_single_tool', 'location': ('tests/test_pack.py', 67, 'test_pack_single_tool'), 'keywords': {'test_pack_single_tool': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00024069299979601055, 'start': 1685951452.816771, 'stop': 1685951452.817013, '$report_type': 'TestReport', 'item_index': 485, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/%E2%98%95%F0%9F%98%8D",\n "basename": "☕ðŸ˜",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmptyp89s5l\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptyp89s5l\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6462540919992534, 'start': 1685951452.424056, 'stop': 1685951453.070296, '$report_type': 'TestReport', 'item_index': 508, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_output_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/%E2%98%95%F0%9F%98%8D",\n "basename": "☕ðŸ˜",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmptyp89s5l\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test"\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u2615\\ud83d\\ude0d"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test",\n "dirname": "/private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmptyp89s5l$ cat \\\n /private/tmp/docker_tmperyvntaa/stg4d805dbc-ea8b-40e1-a451-4bcd4d16a994/test > /private/tmp/docker_tmptyp89s5l/☕ðŸ˜\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmptyp89s5l/%E2%98%95%F0%9F%98%8D",\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmperyvntaa\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmpsjzkp1vi\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmptyp89s5l/☕😠to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__3/outdir/☕ðŸ˜\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmptyp89s5l\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006110310005169595, 'start': 1685951453.071579, 'stop': 1685951453.072191, '$report_type': 'TestReport', 'item_index': 508, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u2615\U0001f60d] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u2615\\U0001f60d]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]'), 'keywords': {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015628669998477562, 'start': 1685951453.07393, 'stop': 1685951453.0754938, '$report_type': 'TestReport', 'item_index': 509, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_single_tool', 'location': ('tests/test_pack.py', 67, 'test_pack_single_tool'), 'keywords': {'test_pack_single_tool': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl'")], 'duration': 0.26076059300066845, 'start': 1685951452.8174798, 'stop': 1685951453.078235, '$report_type': 'TestReport', 'item_index': 485, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_single_tool', 'location': ('tests/test_pack.py', 67, 'test_pack_single_tool'), 'keywords': {'test_pack_single_tool': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/formattest.cwl'")], 'duration': 0.0001997359995584702, 'start': 1685951453.0787358, 'stop': 1685951453.078937, '$report_type': 'TestReport', 'item_index': 485, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_pack_single_tool - location: ('tests/test_pack.py', 67, 'test_pack_single_tool') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_fragment', 'location': ('tests/test_pack.py', 79, 'test_pack_fragment'), 'keywords': {'test_pack_fragment': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00020665400006691925, 'start': 1685951453.0797708, 'stop': 1685951453.079979, '$report_type': 'TestReport', 'item_index': 486, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pack.py::test_pack_fragment - location: ('tests/test_pack.py', 79, 'test_pack_fragment') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_parallel.py::test_scattered_workflow', 'location': ('tests/test_parallel.py', 23, 'test_scattered_workflow'), 'keywords': {'test_scattered_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] inputs {\n "inp1": [\n "one",\n "two"\n ],\n "inp2": [\n "three",\n "four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] starting step step1_4\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] {\n "echo_in1": "one",\n "echo_in2": "three"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "one"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "three"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_4), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_4] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo$ echo \\\n -n \\\n foo \\\n one \\\n three > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo/step1_out\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] {\n "echo_in1": "two",\n "echo_in2": "four"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "two"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "four"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_5), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_$ echo \\\n -n \\\n foo \\\n two \\\n four > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_/step1_out\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_4] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] outputs {\n "echo_out": "foo one three"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/7k412rnh\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/wm12k6ms\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_5] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] outputs {\n "echo_out": "foo two four"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo one three",\n "foo two four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] outputs {\n "out": [\n "foo one three",\n "foo two four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h4t3gb09\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/302zkbup\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pu7_apaa\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\nDEBUG cwltool:workflow_job.py:777 [workflow _6] inputs {\n "inp1": [\n "one",\n "two"\n ],\n "inp2": [\n "three",\n "four"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _6] starting step step1_4\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:75 [step step1_4] start\nINFO cwltool:workflow_job.py:765 [workflow _6] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_4] {\n "echo_in1": "one",\n "echo_in2": "three"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "one"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "three"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_4), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:job.py:215 [job step1_4] initial work dir {}\nINFO cwltool:job.py:266 [job step1_4] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo$ echo \\\n -n \\\n foo \\\n one \\\n three > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo/step1_out\nDEBUG cwltool:command_line_tool.py:982 [job step1_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:988 [job step1_5] {\n "echo_in1": "two",\n "echo_in2": "four"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "two"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "four"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_5), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job step1_5] initial work dir {}\nINFO cwltool:job.py:266 [job step1_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_$ echo \\\n -n \\\n foo \\\n two \\\n four > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_/step1_out\nINFO cwltool:job.py:419 [job step1_4] completed success\nDEBUG cwltool:job.py:422 [job step1_4] outputs {\n "echo_out": "foo one three"\n}\nDEBUG cwltool:job.py:446 [job step1_4] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/7k412rnh\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:job.py:454 [job step1_4] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/wm12k6ms\nINFO cwltool:job.py:419 [job step1_5] completed success\nDEBUG cwltool:job.py:422 [job step1_5] outputs {\n "echo_out": "foo two four"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo one three",\n "foo two four"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _6] outputs {\n "out": [\n "foo one three",\n "foo two four"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h4t3gb09\nDEBUG cwltool:job.py:454 [job step1_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/302zkbup\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pu7_apaa\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_')], 'duration': 0.8109973410000748, 'start': 1685951452.437483, 'stop': 1685951453.248462, '$report_type': 'TestReport', 'item_index': 495, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_parallel.py::test_scattered_workflow', 'location': ('tests/test_parallel.py', 23, 'test_scattered_workflow'), 'keywords': {'test_scattered_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_parallel.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:52]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] inputs {\n "inp1": [\n "one",\n "two"\n ],\n "inp2": [\n "three",\n "four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] starting step step1_4\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: , runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] {\n "echo_in1": "one",\n "echo_in2": "three"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "one"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "three"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_4), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_4] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo$ echo \\\n -n \\\n foo \\\n one \\\n three > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo/step1_out\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] {\n "echo_in1": "two",\n "echo_in2": "four"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] path mappings is {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "two"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "four"\n }\n]\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mjob: CommandLineJob(step1_5), runtime_context: , TMPDIR_LOCK: \x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] initial work dir {}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_$ echo \\\n -n \\\n foo \\\n two \\\n four > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_/step1_out\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_4] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] outputs {\n "echo_out": "foo one three"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/7k412rnh\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_4] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/wm12k6ms\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [job step1_5] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] outputs {\n "echo_out": "foo two four"\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo one three",\n "foo two four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [step step1_4] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m [workflow _6] completed success\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _6] outputs {\n "out": [\n "foo one three",\n "foo two four"\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h4t3gb09\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/302zkbup\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pu7_apaa\x1b[0m\n\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_\x1b[0m\n'), ('Captured log call', 'INFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _6] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\nDEBUG cwltool:workflow_job.py:777 [workflow _6] inputs {\n "inp1": [\n "one",\n "two"\n ],\n "inp2": [\n "three",\n "four"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _6] starting step step1_4\nDEBUG cwltool:executors.py:309 job: , runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:75 [step step1_4] start\nINFO cwltool:workflow_job.py:765 [workflow _6] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_4] {\n "echo_in1": "one",\n "echo_in2": "three"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "one"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "three"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_4), runtime_context: , TMPDIR_LOCK: \nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:job.py:215 [job step1_4] initial work dir {}\nINFO cwltool:job.py:266 [job step1_4] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo$ echo \\\n -n \\\n foo \\\n one \\\n three > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo/step1_out\nDEBUG cwltool:command_line_tool.py:982 [job step1_5] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_4\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:command_line_tool.py:988 [job step1_5] {\n "echo_in1": "two",\n "echo_in2": "four"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_5] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "two"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "four"\n }\n]\nDEBUG cwltool:executors.py:309 job: CommandLineJob(step1_5), runtime_context: , TMPDIR_LOCK: \nDEBUG cwltool:job.py:215 [job step1_5] initial work dir {}\nINFO cwltool:job.py:266 [job step1_5] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_$ echo \\\n -n \\\n foo \\\n two \\\n four > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_/step1_out\nINFO cwltool:job.py:419 [job step1_4] completed success\nDEBUG cwltool:job.py:422 [job step1_4] outputs {\n "echo_out": "foo one three"\n}\nDEBUG cwltool:job.py:446 [job step1_4] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/7k412rnh\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:job.py:454 [job step1_4] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/wm12k6ms\nINFO cwltool:job.py:419 [job step1_5] completed success\nDEBUG cwltool:job.py:422 [job step1_5] outputs {\n "echo_out": "foo two four"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo one three",\n "foo two four"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _6] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _6] outputs {\n "out": [\n "foo one three",\n "foo two four"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_5] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/h4t3gb09\nDEBUG cwltool:job.py:454 [job step1_5] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/302zkbup\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/zmvl38vo\nDEBUG cwltool:process.py:398 Removing intermediate output directory /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pu7_apaa\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/2xkys07_')], 'duration': 0.0004042090004077181, 'start': 1685951453.249595, 'stop': 1685951453.250001, '$report_type': 'TestReport', 'item_index': 495, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_parallel.py::test_scattered_workflow - location: ('tests/test_parallel.py', 23, 'test_scattered_workflow') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_spaces_in_input_files - location: ('tests/test_path_checks.py', 39, 'test_spaces_in_input_files') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_spaces_in_input_files', 'location': ('tests/test_path_checks.py', 39, 'test_spaces_in_input_files'), 'keywords': {'test_spaces_in_input_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013412010002866737, 'start': 1685951453.253155, 'stop': 1685951453.254497, '$report_type': 'TestReport', 'item_index': 496, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_require_prefix_workreuse', 'location': ('tests/test_ext.py', 241, 'test_require_prefix_workreuse'), 'keywords': {'test_require_prefix_workreuse': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "page": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt",\n "basename": "time.txt",\n "class": "File",\n "checksum": "sha1$2682bb62398b0d95b2086661579b252fe8c8667c",\n "size": 19,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl'\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] /private/tmp/docker_tmpaadyphdc$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpaadyphdc,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp5uqhdbo1,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpz_91s5q9/20230605095051-050288.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n 'import time\nprint(time.time())\n' > /private/tmp/docker_tmpaadyphdc/time.txt\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/workreuse.cwl:6:1: checking field 'requirements'\ntests/wf/workreuse.cwl:9:3: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#WorkReuse'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/workreuse-fail.cwl:4:1: checking field 'requirements'\ntests/wf/workreuse-fail.cwl:7:3: checking item\n Field 'class' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/WorkReuse'\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job workreuse.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\nDEBUG cwltool:command_line_tool.py:988 [job workreuse.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job workreuse.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job workreuse.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "valueFrom": "import time\\nprint(time.time())\\n",\n "position": [\n 0,\n 1\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job workreuse.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job workreuse.cwl] /private/tmp/docker_tmpaadyphdc$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpaadyphdc,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp5uqhdbo1,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpz_91s5q9/20230605095051-050288.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import time\nprint(time.time())\n\' > /private/tmp/docker_tmpaadyphdc/time.txt\nINFO cwltool:job.py:905 [job workreuse.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job workreuse.cwl] completed success\nDEBUG cwltool:job.py:422 [job workreuse.cwl] outputs {\n "page": {\n "location": "file:///private/tmp/docker_tmpaadyphdc/time.txt",\n "basename": "time.txt",\n "nameroot": "time",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$2682bb62398b0d95b2086661579b252fe8c8667c",\n "size": 19,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job workreuse.cwl] Removing input staging directory /private/tmp/docker_tmpa6x0fmbj\nDEBUG cwltool:job.py:454 [job workreuse.cwl] Removing temporary directory /private/tmp/docker_tmp5uqhdbo1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpaadyphdc/time.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaadyphdc\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/workreuse.cwl:6:1: checking field \'requirements\'\ntests/wf/workreuse.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#WorkReuse\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/workreuse-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/workreuse-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/WorkReuse\'')], 'duration': 3.239526761999514, 'start': 1685951450.218237, 'stop': 1685951453.457684, '$report_type': 'TestReport', 'item_index': 377, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_ext.py::test_require_prefix_workreuse', 'location': ('tests/test_ext.py', 241, 'test_require_prefix_workreuse'), 'keywords': {'test_require_prefix_workreuse': 1, 'skipif': 1, 'pytestmark': 1, 'test_ext.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "page": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt",\n "basename": "time.txt",\n "class": "File",\n "checksum": "sha1$2682bb62398b0d95b2086661579b252fe8c8667c",\n "size": 19,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl'\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] /private/tmp/docker_tmpaadyphdc$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpaadyphdc,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp5uqhdbo1,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpz_91s5q9/20230605095051-050288.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n 'import time\nprint(time.time())\n' > /private/tmp/docker_tmpaadyphdc/time.txt\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job workreuse.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/workreuse.cwl:6:1: checking field 'requirements'\ntests/wf/workreuse.cwl:9:3: checking item\n Field 'class' contains undefined reference to\n 'http://commonwl.org/cwltool#WorkReuse'\x1b[0m\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mTool definition failed validation:\ntests/wf/workreuse-fail.cwl:4:1: checking field 'requirements'\ntests/wf/workreuse-fail.cwl:7:3: checking item\n Field 'class' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/WorkReuse'\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job workreuse.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\nDEBUG cwltool:command_line_tool.py:988 [job workreuse.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job workreuse.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job workreuse.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "valueFrom": "import time\\nprint(time.time())\\n",\n "position": [\n 0,\n 1\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job workreuse.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job workreuse.cwl] /private/tmp/docker_tmpaadyphdc$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpaadyphdc,target=/hPkhbA \\\n --mount=type=bind,source=/private/tmp/docker_tmp5uqhdbo1,target=/tmp \\\n --workdir=/hPkhbA \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpz_91s5q9/20230605095051-050288.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/hPkhbA \\\n docker.io/python:3-slim \\\n python \\\n -c \\\n \'import time\nprint(time.time())\n\' > /private/tmp/docker_tmpaadyphdc/time.txt\nINFO cwltool:job.py:905 [job workreuse.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job workreuse.cwl] completed success\nDEBUG cwltool:job.py:422 [job workreuse.cwl] outputs {\n "page": {\n "location": "file:///private/tmp/docker_tmpaadyphdc/time.txt",\n "basename": "time.txt",\n "nameroot": "time",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$2682bb62398b0d95b2086661579b252fe8c8667c",\n "size": 19,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job workreuse.cwl] Removing input staging directory /private/tmp/docker_tmpa6x0fmbj\nDEBUG cwltool:job.py:454 [job workreuse.cwl] Removing temporary directory /private/tmp/docker_tmp5uqhdbo1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpaadyphdc/time.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_require_prefix_workreuse0/time.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpaadyphdc\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/workreuse.cwl:6:1: checking field \'requirements\'\ntests/wf/workreuse.cwl:9:3: checking item\n Field \'class\' contains undefined reference to\n \'http://commonwl.org/cwltool#WorkReuse\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/workreuse-fail.cwl\'\nERROR cwltool:main.py:1208 Tool definition failed validation:\ntests/wf/workreuse-fail.cwl:4:1: checking field \'requirements\'\ntests/wf/workreuse-fail.cwl:7:3: checking item\n Field \'class\' contains undefined reference to\n \'file:///Users/jasperk/gitlab/cwltool/tests/wf/WorkReuse\'')], 'duration': 0.0004003159992862493, 'start': 1685951453.458577, 'stop': 1685951453.458978, '$report_type': 'TestReport', 'item_index': 377, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_ext.py::test_require_prefix_workreuse - location: ('tests/test_ext.py', 241, 'test_require_prefix_workreuse') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u6e2c\u8a66] - location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u6e2c\\u8a66]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u6e2c\\u8a66]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u6e2c\\u8a66]'), 'keywords': {'test_unicode_in_input_files[\\u6e2c\\u8a66]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u6e2c\\u8a66': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013005709997742088, 'start': 1685951453.460156, 'stop': 1685951453.461458, '$report_type': 'TestReport', 'item_index': 497, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_hello_single_tool', 'location': ('tests/test_provenance.py', 61, 'test_hello_single_tool'), 'keywords': {'test_hello_single_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl --message Hello tool\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwmeaibo9/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/tmp/docker_tmpjhr7n0cf$ echo \\\n 'Hello tool'\nHello tool\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl --message Hello tool\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\', job_order=[\'--message\', \'Hello tool\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 70dfb26d3325ac63dd94ae620a2af975f669a90e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 533cc58046d17fc0a7016e4c766c10142ecde5fa38aa18dcf974157d580deb4f workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 3bafbb8b5344c26c18de21b65a086a57982365963bf5002ee8d97e34474d2073db852be7d53e773abe848c43fc1f94107d0aa289a681eb180c03a0e2f9ad7b2d workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwmeaibo9/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello tool"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello tool"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello tool"\n }\n]\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/manifest-sha1.txt: a1e591e931fd3bf502a5124e6cdfccee57cf2c8c data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'message\': \'Hello tool\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello tool\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b7bf61dc3c35c1498e63eab30868107dfd3a0e3c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 7b2e41cde05165fb347d46aeb0515678bdb26a3afcdf0be5e1856c7bed8d634d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 37966e8e9fcb932ac3e0f42ff1a18cb5636fa4ac7bcd58efc93db68c746020472f52de406f4b0bd9b52081f61493af76598749efb026bde8e905b993748aeca5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/tmp/docker_tmpjhr7n0cf$ echo \\\n \'Hello tool\'\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/tmp/docker_tmphhy0qgsq\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/tmp/docker_tmp52t5g_kl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjhr7n0cf\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 0df78c0814a11a10649539f01d3f1d27889b6982 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 4fbaed3c12a57f76a1945adfb70b50c87abda26a15bfc13c26d8a64d1ac715fb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 2acf5249b3f87fa61ca22b79412d2e60a73158abe39f4733b637bf8dc36e02f69d656af1542b70b8dff22a955018997f8a61a4b5a56b7372f8c9fa620a17ea6a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b8d0757535ab4b44d791c2d0fbb174ffe0020685 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ce34ee00d40e193df72d84d7184b22595933c0f238f37c1219bf89ac68eba656 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: e267b9020c79e53a71b64343147f6d5162c3a99597d30968ff7fb98ea24129d775422ea7d8be49c4c9506eb8dca960579135e6a6a1a64d772eb64e0b16c51fcc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b4e90a53e0b472130f1c3bb560a913442f3a47ae metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 51af6b9c16424ec42ee90345fdff5ebdfcc2bec9e0bc8d36bdeefe1615b4a55e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: bcc6d25297dbb1fd15fa5c16d6efbe09a7a171aa9ef096706e800d69abd37d790e7ba6b4cf5837969ffeeb36bb52d8c9ad5a01426e35b253e87d7a9367a59c5e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 1f424d204810cc521f65846029233e67a5aecabc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 6712976929fece3a8fd0c89d00625979ba4a55924d6255e0811e72f81c619e2a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: ce2958adaabaea084457006ce34504167cc4b62fed03866acf3ceac0698696db88b8c50caab76154d46981d65fc47993c872d71b8e535158e2f37ca62bc78d83 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: bf91f553672e8e589844171b3eb1a30b09ff30f4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 0ef0ec1f212396cb7142ad4c56de9ca104789b773e15374625c33ca2eea2cadd metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 7dc7bf8259d4ceee588781512469d2e652993e27efa379530596969764d17f1800bdfccb0183d89ba5f3246418bb5ff9ae8e6b8f96299424c4c9f8f5888c32c4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 8bb1519e84453a0303586ecec455a1ab3a1c065b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ce41810d86d8a98ff8dfc2daa5f48418d88001ff2514fe073d4ae6772f5eb569 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: c049305651d388979433c9ae5743b2a028f9f1f8d5911032d924af95fc18c332f78bb69b76445dab3bfecd3da1588372372e9df75c1a612d3a72f633e3866b36 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: bafd8051fd348d6f5a46c638d04450aaec30077f snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 25bfc086e95b92a670c70b9557b42f18f435538008b32350992929a8340affee snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 5e073bc15f1f665f8e28f397c7eac8db6540a5680d19fb87babdfafafe54c01addbc9c0baebc8f5dd9502a441a6fc052378dfbf35773a9cbde2dc16237229c53 snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 9cf58fb7f38279c7e6a34c35961cc01b715dfcea metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 5455ced4b8f23a5656c8433bc0ca86109cbf855efef98c5ff418c3234b7d1b0a metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: e5a1b7a84990feb5fd2f548e6332edbeb1fa1be639757850234bb1dc7ec3c654eb3390ae564f79093caf7aa1a7f10810637f9770e03cdfbfb6d59d82cf4556d4 metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 6645a7d99f8f1cc1da9f4fa5d08397781becbf60 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 41488aa18839c4e43d13985e1798726007163b9257e571cabfdc85603eeb8aaf metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 6af087ee91140194d771105e4fb6d02fca6b69a1305177e56bd9c317f02b8a847eacd7274937809cf0a5f413d60aff0dcce67ac1881519adb865e305122f5a2d metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 86b54373840e653bd1eb0e225ee28d33f12fc74d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: e1c4900574a6d9f1e46ab83d3fc9fde47b51d5ae343aff9302fb99aeb68f6918 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 2476349f33e8a55648fbf251e53a5ca948b6a79deae8cd94df3e744ce8672f42ec24643fb45884e6cfed9a94282e517e0544a5238397d288eb99fdb21b70a5e6 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance')], 'duration': 0.8588609070002349, 'start': 1685951452.77656, 'stop': 1685951453.635401, '$report_type': 'TestReport', 'item_index': 524, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_hello_single_tool', 'location': ('tests/test_provenance.py', 61, 'test_hello_single_tool'), 'keywords': {'test_hello_single_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl --message Hello tool\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwmeaibo9/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/tmp/docker_tmpjhr7n0cf$ echo \\\n 'Hello tool'\nHello tool\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl --message Hello tool\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\', job_order=[\'--message\', \'Hello tool\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 70dfb26d3325ac63dd94ae620a2af975f669a90e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 533cc58046d17fc0a7016e4c766c10142ecde5fa38aa18dcf974157d580deb4f workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 3bafbb8b5344c26c18de21b65a086a57982365963bf5002ee8d97e34474d2073db852be7d53e773abe848c43fc1f94107d0aa289a681eb180c03a0e2f9ad7b2d workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpwmeaibo9/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello tool"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello tool"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello tool"\n }\n]\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/manifest-sha1.txt: a1e591e931fd3bf502a5124e6cdfccee57cf2c8c data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'message\': \'Hello tool\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello tool\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b7bf61dc3c35c1498e63eab30868107dfd3a0e3c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 7b2e41cde05165fb347d46aeb0515678bdb26a3afcdf0be5e1856c7bed8d634d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 37966e8e9fcb932ac3e0f42ff1a18cb5636fa4ac7bcd58efc93db68c746020472f52de406f4b0bd9b52081f61493af76598749efb026bde8e905b993748aeca5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/tmp/docker_tmpjhr7n0cf$ echo \\\n \'Hello tool\'\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a1/a1e591e931fd3bf502a5124e6cdfccee57cf2c8c\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/tmp/docker_tmphhy0qgsq\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/tmp/docker_tmp52t5g_kl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjhr7n0cf\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 0df78c0814a11a10649539f01d3f1d27889b6982 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 4fbaed3c12a57f76a1945adfb70b50c87abda26a15bfc13c26d8a64d1ac715fb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 2acf5249b3f87fa61ca22b79412d2e60a73158abe39f4733b637bf8dc36e02f69d656af1542b70b8dff22a955018997f8a61a4b5a56b7372f8c9fa620a17ea6a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b8d0757535ab4b44d791c2d0fbb174ffe0020685 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ce34ee00d40e193df72d84d7184b22595933c0f238f37c1219bf89ac68eba656 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: e267b9020c79e53a71b64343147f6d5162c3a99597d30968ff7fb98ea24129d775422ea7d8be49c4c9506eb8dca960579135e6a6a1a64d772eb64e0b16c51fcc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: b4e90a53e0b472130f1c3bb560a913442f3a47ae metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 51af6b9c16424ec42ee90345fdff5ebdfcc2bec9e0bc8d36bdeefe1615b4a55e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: bcc6d25297dbb1fd15fa5c16d6efbe09a7a171aa9ef096706e800d69abd37d790e7ba6b4cf5837969ffeeb36bb52d8c9ad5a01426e35b253e87d7a9367a59c5e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 1f424d204810cc521f65846029233e67a5aecabc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 6712976929fece3a8fd0c89d00625979ba4a55924d6255e0811e72f81c619e2a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: ce2958adaabaea084457006ce34504167cc4b62fed03866acf3ceac0698696db88b8c50caab76154d46981d65fc47993c872d71b8e535158e2f37ca62bc78d83 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: bf91f553672e8e589844171b3eb1a30b09ff30f4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 0ef0ec1f212396cb7142ad4c56de9ca104789b773e15374625c33ca2eea2cadd metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 7dc7bf8259d4ceee588781512469d2e652993e27efa379530596969764d17f1800bdfccb0183d89ba5f3246418bb5ff9ae8e6b8f96299424c4c9f8f5888c32c4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 8bb1519e84453a0303586ecec455a1ab3a1c065b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ce41810d86d8a98ff8dfc2daa5f48418d88001ff2514fe073d4ae6772f5eb569 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: c049305651d388979433c9ae5743b2a028f9f1f8d5911032d924af95fc18c332f78bb69b76445dab3bfecd3da1588372372e9df75c1a612d3a72f633e3866b36 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: bafd8051fd348d6f5a46c638d04450aaec30077f snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 25bfc086e95b92a670c70b9557b42f18f435538008b32350992929a8340affee snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 5e073bc15f1f665f8e28f397c7eac8db6540a5680d19fb87babdfafafe54c01addbc9c0baebc8f5dd9502a441a6fc052378dfbf35773a9cbde2dc16237229c53 snapshot/hello_single_tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 9cf58fb7f38279c7e6a34c35961cc01b715dfcea metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 5455ced4b8f23a5656c8433bc0ca86109cbf855efef98c5ff418c3234b7d1b0a metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: e5a1b7a84990feb5fd2f548e6332edbeb1fa1be639757850234bb1dc7ec3c654eb3390ae564f79093caf7aa1a7f10810637f9770e03cdfbfb6d59d82cf4556d4 metadata/logs/engine.4952b59e-9213-4a15-959f-ee25269247a9.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 6645a7d99f8f1cc1da9f4fa5d08397781becbf60 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: 41488aa18839c4e43d13985e1798726007163b9257e571cabfdc85603eeb8aaf metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 6af087ee91140194d771105e4fb6d02fca6b69a1305177e56bd9c317f02b8a847eacd7274937809cf0a5f413d60aff0dcce67ac1881519adb865e305122f5a2d metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha1.txt: 86b54373840e653bd1eb0e225ee28d33f12fc74d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha256.txt: e1c4900574a6d9f1e46ab83d3fc9fde47b51d5ae343aff9302fb99aeb68f6918 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut/tagmanifest-sha512.txt: 2476349f33e8a55648fbf251e53a5ca948b6a79deae8cd94df3e744ce8672f42ec24643fb45884e6cfed9a94282e517e0544a5238397d288eb99fdb21b70a5e6 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/8ecvgwut\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_hello_single_tool0/provenance')], 'duration': 0.0006209440007296507, 'start': 1685951453.636877, 'stop': 1685951453.6374998, '$report_type': 'TestReport', 'item_index': 524, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_hello_single_tool - location: ('tests/test_provenance.py', 61, 'test_hello_single_tool') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - when: runtest - nodeid: tests/test_provenance.py::test_hello_single_tool - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_revsort_workflow - location: ('tests/test_provenance.py', 74, 'test_revsort_workflow') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow', 'location': ('tests/test_provenance.py', 74, 'test_revsort_workflow'), 'keywords': {'test_revsort_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011466310006653657, 'start': 1685951453.639364, 'stop': 1685951453.640511, '$report_type': 'TestReport', 'item_index': 525, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]'), 'keywords': {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "امتحان",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpu7fd0k2e\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu7fd0k2e\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6586480109999684, 'start': 1685951453.075871, 'stop': 1685951453.734503, '$report_type': 'TestReport', 'item_index': 509, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]'), 'keywords': {'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "امتحان",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpu7fd0k2e\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test"\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test",\n "dirname": "/private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmpu7fd0k2e$ cat \\\n /private/tmp/docker_tmpj02o4uuh/stg7619f146-05be-426c-9b88-1faecc5c8c4e/test > /private/tmp/docker_tmpu7fd0k2e/امتحان\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpu7fd0k2e/%D8%A7%D9%85%D8%AA%D8%AD%D8%A7%D9%86",\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpj02o4uuh\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpn4v470d8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu7fd0k2e/امتحان to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files__4/outdir/امتحان\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu7fd0k2e\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005586230008702842, 'start': 1685951453.7356002, 'stop': 1685951453.736159, '$report_type': 'TestReport', 'item_index': 509, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u0627\u0645\u062a\u062d\u0627\u0646] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013699379996978678, 'start': 1685951453.7374332, 'stop': 1685951453.7388039, '$report_type': 'TestReport', 'item_index': 510, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_fragment', 'location': ('tests/test_pack.py', 79, 'test_pack_fragment'), 'keywords': {'test_pack_fragment': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl'\nURI prefix 'keep' of 'keep:99999999999999999999999999999999+118/token.txt' not recognized, are you missing a $namespaces section?\ntests/wf/scatter2.cwl:18:7: Warning: Unsupported scheme 'keep' in url:\n keep:99999999999999999999999999999999+118/token.txt\ntests/wf/scatter2.cwl:36:9: Warning: checking item\n Warning: Field 'class' contains undefined reference to\n 'http://arvados.org/cwl#RunInSingleContainer'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'keep' of 'keep:99999999999999999999999999999999+118/token.txt' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1157 tests/wf/scatter2.cwl:18:7: Warning: Unsupported scheme 'keep' in url:\n keep:99999999999999999999999999999999+118/token.txt\nWARNING salad:ref_resolver.py:1157 tests/wf/scatter2.cwl:36:9: Warning: checking item\n Warning: Field 'class' contains undefined reference to\n 'http://arvados.org/cwl#RunInSingleContainer'")], 'duration': 0.7120275979996222, 'start': 1685951453.0802948, 'stop': 1685951453.792306, '$report_type': 'TestReport', 'item_index': 486, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_fragment', 'location': ('tests/test_pack.py', 79, 'test_pack_fragment'), 'keywords': {'test_pack_fragment': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl'\nURI prefix 'keep' of 'keep:99999999999999999999999999999999+118/token.txt' not recognized, are you missing a $namespaces section?\ntests/wf/scatter2.cwl:18:7: Warning: Unsupported scheme 'keep' in url:\n keep:99999999999999999999999999999999+118/token.txt\ntests/wf/scatter2.cwl:36:9: Warning: checking item\n Warning: Field 'class' contains undefined reference to\n 'http://arvados.org/cwl#RunInSingleContainer'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter2.cwl'\nWARNING salad:ref_resolver.py:240 URI prefix 'keep' of 'keep:99999999999999999999999999999999+118/token.txt' not recognized, are you missing a $namespaces section?\nWARNING salad:ref_resolver.py:1157 tests/wf/scatter2.cwl:18:7: Warning: Unsupported scheme 'keep' in url:\n keep:99999999999999999999999999999999+118/token.txt\nWARNING salad:ref_resolver.py:1157 tests/wf/scatter2.cwl:36:9: Warning: checking item\n Warning: Field 'class' contains undefined reference to\n 'http://arvados.org/cwl#RunInSingleContainer'")], 'duration': 0.00022919200000615092, 'start': 1685951453.792846, 'stop': 1685951453.793076, '$report_type': 'TestReport', 'item_index': 486, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pack.py::test_pack_fragment - location: ('tests/test_pack.py', 79, 'test_pack_fragment') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 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pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pack.py::test_pack_rewrites', 'location': ('tests/test_pack.py', 96, 'test_pack_rewrites'), 'keywords': {'test_pack_rewrites': 1, 'test_pack.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:53]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default-wf5.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default-wf5.cwl'\ntests/wf/default-dir5.cwl:20:13: Warning: Field 'location' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/inp1'\ntests/wf/default-dir5.cwl:20:13: Warning: Field 'location' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/inp1'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved 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/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpfc21sv3y\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6394740679997994, 'start': 1685951453.461801, 'stop': 1685951454.1012611, '$report_type': 'TestReport', 'item_index': 497, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 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'tests/test_path_checks.py::test_unicode_in_input_files[\\uadf8\\ub798\\ud504]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]'), 'keywords': {'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0020320819994594785, 'start': 1685951454.104286, 'stop': 1685951454.10632, '$report_type': 'TestReport', 'item_index': 498, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj2n4e2tf\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj2n4e2tf\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6722589929995593, 'start': 1685951453.739232, 'stop': 1685951454.411476, '$report_type': 'TestReport', 'item_index': 510, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_output_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj2n4e2tf\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test"\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "abc+DEFGZ.z_12345-"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test",\n "dirname": "/private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj2n4e2tf$ cat \\\n /private/tmp/docker_tmp6m4yfwbs/stg5f021d42-1b0f-4853-a35c-8cedf6e05ac9/test > /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345-\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj2n4e2tf/abc%2BDEFGZ.z_12345-",\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmp6m4yfwbs\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmp_upmz18_\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj2n4e2tf/abc+DEFGZ.z_12345- to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_unicode_in_output_files_a0/outdir/abc+DEFGZ.z_12345-\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj2n4e2tf\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0010611549996610847, 'start': 1685951454.412545, 'stop': 1685951454.4136078, '$report_type': 'TestReport', 'item_index': 510, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[abc+DEFGZ.z_12345-] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[abc+DEFGZ.z_12345-]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names - location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_clt_returns_specialchar_names', 'location': ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names'), 'keywords': {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001187488999676134, 'start': 1685951454.415158, 'stop': 1685951454.416346, '$report_type': 'TestReport', 'item_index': 511, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_clt_returns_specialchar_names', 'location': ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names'), 'keywords': {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0065578280000408995, 'start': 1685951454.416679, 'stop': 1685951454.4232378, '$report_type': 'TestReport', 'item_index': 511, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_clt_returns_specialchar_names', 'location': ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names'), 'keywords': {'test_clt_returns_specialchar_names': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002504579997548717, 'start': 1685951454.423627, 'stop': 1685951454.423879, '$report_type': 'TestReport', 'item_index': 511, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_clt_returns_specialchar_names - location: ('tests/test_path_checks.py', 129, 'test_clt_returns_specialchar_names') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_pathmapper.py::test_subclass - location: ('tests/test_pathmapper.py', 8, 'test_subclass') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_subclass', 'location': ('tests/test_pathmapper.py', 8, 'test_subclass'), 'keywords': {'test_subclass': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00020675299947470194, 'start': 1685951454.4253829, 'stop': 1685951454.425591, '$report_type': 'TestReport', 'item_index': 512, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_subclass', 'location': ('tests/test_pathmapper.py', 8, 'test_subclass'), 'keywords': {'test_subclass': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00025883699981932295, 'start': 1685951454.4258912, 'stop': 1685951454.4261508, '$report_type': 'TestReport', 'item_index': 512, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_pathmapper.py::test_subclass', 'location': ('tests/test_pathmapper.py', 8, 'test_subclass'), 'keywords': {'test_subclass': 1, 'test_pathmapper.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00017651699999987613, 'start': 1685951454.426451, 'stop': 1685951454.426628, '$report_type': 'TestReport', 'item_index': 512, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_pathmapper.py::test_subclass - location: ('tests/test_pathmapper.py', 8, 'test_subclass') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_secrets.py::test_secrets[-expected1] - location: ('tests/test_secrets.py', 40, 'test_secrets[-expected1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected1]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected1]'), 'keywords': {'test_secrets[-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected1': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0007169380005507264, 'start': 1685951454.427757, 'stop': 1685951454.4284759, '$report_type': 'TestReport', 'item_index': 581, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> -expected1]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -expected1]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: -expected1]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected1]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected1]'), 'keywords': {'test_secrets[-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected1': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.000249826000072062, 'start': 1685951454.42887, 'stop': 1685951454.429121, '$report_type': 'TestReport', 'item_index': 581, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> -expected1]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -expected1]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: -expected1]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected1]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected1]'), 'keywords': {'test_secrets[-expected1]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected1': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002683279999473598, 'start': 1685951454.429458, 'stop': 1685951454.429728, '$report_type': 'TestReport', 'item_index': 581, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> -expected1]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -expected1]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: -expected1]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_secrets.py::test_secrets[-expected1] - location: ('tests/test_secrets.py', 40, 'test_secrets[-expected1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_secrets.py::test_secrets[-expected2] - location: ('tests/test_secrets.py', 40, 'test_secrets[-expected2]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected2]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected2]'), 'keywords': {'test_secrets[-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected2': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006197129996508011, 'start': 1685951454.4304729, 'stop': 1685951454.431094, '$report_type': 'TestReport', 'item_index': 582, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> -expected2]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -expected2]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: -expected2]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected2]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected2]'), 'keywords': {'test_secrets[-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected2': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0003470820001894026, 'start': 1685951454.431703, 'stop': 1685951454.432051, '$report_type': 'TestReport', 'item_index': 582, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> -expected2]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -expected2]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: -expected2]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secrets[-expected2]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-expected2]'), 'keywords': {'test_secrets[-expected2]': 1, 'parametrize': 1, 'pytestmark': 1, '-expected2': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0004827409993595211, 'start': 1685951454.432508, 'stop': 1685951454.432993, '$report_type': 'TestReport', 'item_index': 582, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> -expected2]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -expected2]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: -expected2]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_secrets.py::test_secrets[-expected2] - location: ('tests/test_secrets.py', 40, 'test_secrets[-expected2]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_secrets.py::test_secret_workflow_log - location: ('tests/test_secrets.py', 59, 'test_secret_workflow_log') - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log', 'location': ('tests/test_secrets.py', 59, 'test_secret_workflow_log'), 'keywords': {'test_secret_workflow_log': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00021649700011039386, 'start': 1685951454.433845, 'stop': 1685951454.434062, '$report_type': 'TestReport', 'item_index': 583, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_spaces_in_input_files', 'location': ('tests/test_path_checks.py', 39, 'test_spaces_in_input_files'), 'keywords': {'test_spaces_in_input_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error:\nInvalid filename: \'test with spaces\' contains illegal characters\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1315, in main\n (out, status) = real_executor(\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 61, in __call__\n return self.execute(process, job_order_object, runtime_context, logger)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 144, in execute\n self.run_jobs(process, job_order_object, logger, runtime_context)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 217, in run_jobs\n for job in jobiter:\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 995, in job\n visit_class([builder.files, builder.bindings], ("File", "Directory"), _check_adjust)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 379, in check_adjust\n raise WorkflowException(\ncwltool.errors.WorkflowException: Invalid filename: \'test with spaces\' contains illegal characters\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": "",\n "path": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "dirname": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmpjob2jn5j$ cat \\\n \'/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces\' > /private/tmp/docker_tmpjob2jn5j/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjob2jn5j/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmp0vvpiege\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp6fg7354d\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjob2jn5j/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjob2jn5j\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\nDEBUG cwltool:command_line_tool.py:988 [job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\nERROR cwltool:main.py:1380 Workflow error:\nInvalid filename: \'test with spaces\' contains illegal characters\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1315, in main\n (out, status) = real_executor(\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 61, in __call__\n return self.execute(process, job_order_object, runtime_context, logger)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 144, in execute\n self.run_jobs(process, job_order_object, logger, runtime_context)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 217, in run_jobs\n for job in jobiter:\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 995, in job\n visit_class([builder.files, builder.bindings], ("File", "Directory"), _check_adjust)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 379, in check_adjust\n raise WorkflowException(\ncwltool.errors.WorkflowException: Invalid filename: \'test with spaces\' contains illegal characters\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": "",\n "path": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "dirname": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmpjob2jn5j$ cat \\\n \'/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces\' > /private/tmp/docker_tmpjob2jn5j/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjob2jn5j/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmp0vvpiege\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp6fg7354d\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjob2jn5j/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjob2jn5j\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.3361983879995023, 'start': 1685951453.254849, 'stop': 1685951454.591017, '$report_type': 'TestReport', 'item_index': 496, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_spaces_in_input_files', 'location': ('tests/test_path_checks.py', 39, 'test_spaces_in_input_files'), 'keywords': {'test_spaces_in_input_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error:\nInvalid filename: \'test with spaces\' contains illegal characters\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1315, in main\n (out, status) = real_executor(\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 61, in __call__\n return self.execute(process, job_order_object, runtime_context, logger)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 144, in execute\n self.run_jobs(process, job_order_object, logger, runtime_context)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 217, in run_jobs\n for job in jobiter:\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 995, in job\n visit_class([builder.files, builder.bindings], ("File", "Directory"), _check_adjust)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 379, in check_adjust\n raise WorkflowException(\ncwltool.errors.WorkflowException: Invalid filename: \'test with spaces\' contains illegal characters\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": "",\n "path": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "dirname": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmpjob2jn5j$ cat \\\n \'/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces\' > /private/tmp/docker_tmpjob2jn5j/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjob2jn5j/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmp0vvpiege\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmp6fg7354d\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjob2jn5j/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjob2jn5j\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\nDEBUG cwltool:command_line_tool.py:988 [job script] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\nERROR cwltool:main.py:1380 Workflow error:\nInvalid filename: \'test with spaces\' contains illegal characters\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/main.py", line 1315, in main\n (out, status) = real_executor(\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 61, in __call__\n return self.execute(process, job_order_object, runtime_context, logger)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 144, in execute\n self.run_jobs(process, job_order_object, logger, runtime_context)\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 217, in run_jobs\n for job in jobiter:\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 995, in job\n visit_class([builder.files, builder.bindings], ("File", "Directory"), _check_adjust)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 220, in visit_class\n visit_class(d, cls, op)\n File "/Users/jasperk/gitlab/cwltool/cwltool/utils.py", line 215, in visit_class\n op(rec)\n File "/Users/jasperk/gitlab/cwltool/cwltool/command_line_tool.py", line 379, in check_adjust\n raise WorkflowException(\ncwltool.errors.WorkflowException: Invalid filename: \'test with spaces\' contains illegal characters\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/test with spaces",\n "size": 0,\n "basename": "test with spaces",\n "nameroot": "test with spaces",\n "nameext": "",\n "path": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces",\n "dirname": "/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmpjob2jn5j$ cat \\\n \'/private/tmp/docker_tmp0vvpiege/stg92c67f17-044b-4feb-9b7d-36ef2c116f5a/test with spaces\' > /private/tmp/docker_tmpjob2jn5j/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjob2jn5j/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmp0vvpiege\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmp6fg7354d\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjob2jn5j/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_spaces_in_input_files0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjob2jn5j\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.001422736000677105, 'start': 1685951454.592406, 'stop': 1685951454.5938299, '$report_type': 'TestReport', 'item_index': 496, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_spaces_in_input_files - location: ('tests/test_path_checks.py', 39, 'test_spaces_in_input_files') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_recursive_validation.py::test_recursive_validation - location: ('tests/test_recursive_validation.py', 6, 'test_recursive_validation') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_recursive_validation.py::test_recursive_validation', 'location': ('tests/test_recursive_validation.py', 6, 'test_recursive_validation'), 'keywords': {'test_recursive_validation': 1, 'test_recursive_validation.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00027750600020226557, 'start': 1685951454.5955992, 'stop': 1685951454.595878, '$report_type': 'TestReport', 'item_index': 573, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_recursive_validation.py::test_recursive_validation', 'location': ('tests/test_recursive_validation.py', 6, 'test_recursive_validation'), 'keywords': {'test_recursive_validation': 1, 'test_recursive_validation.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:54]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl'\ntests/wf/default_path.cwl:9:7: Warning: Field 'path' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default.txt'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/default_path.cwl:9:7: Warning: Field 'path' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default.txt'")], 'duration': 0.017540503999953216, 'start': 1685951454.59646, 'stop': 1685951454.614002, '$report_type': 'TestReport', 'item_index': 573, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_recursive_validation.py::test_recursive_validation', 'location': ('tests/test_recursive_validation.py', 6, 'test_recursive_validation'), 'keywords': {'test_recursive_validation': 1, 'test_recursive_validation.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:54]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl'\ntests/wf/default_path.cwl:9:7: Warning: Field 'path' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default.txt'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default_path.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/default_path.cwl:9:7: Warning: Field 'path' contains undefined reference to\n 'file:///Users/jasperk/gitlab/cwltool/tests/wf/default.txt'")], 'duration': 0.00020327099991845898, 'start': 1685951454.614452, 'stop': 1685951454.614657, '$report_type': 'TestReport', 'item_index': 573, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_recursive_validation.py::test_recursive_validation - location: ('tests/test_recursive_validation.py', 6, 'test_recursive_validation') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_relocate.py::test_for_910 - location: ('tests/test_relocate.py', 14, 'test_for_910') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_relocate.py::test_for_910', 'location': ('tests/test_relocate.py', 14, 'test_for_910'), 'keywords': {'test_for_910': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0011727219998647342, 'start': 1685951454.615575, 'stop': 1685951454.61675, '$report_type': 'TestReport', 'item_index': 574, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_relocate.py::test_relocate_symlinks', 'location': ('tests/test_relocate.py', 57, 'test_relocate_symlinks'), 'keywords': {'test_relocate_symlinks': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "bar": {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo",\n "basename": "foo",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\ntotal 0\nlrwxr-xr-x 1 jasperk wheel 46 Jun 5 09:50 dir2 -> /Users/jasperk/gitlab/cwltool/tests/reloc/dir2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmphfn_s4u0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\nDEBUG cwltool:command_line_tool.py:988 [job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job test.cwl] completed success\nDEBUG cwltool:job.py:422 [job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\nDEBUG cwltool:job.py:454 [job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmphfn_s4u0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7850257770005555, 'start': 1685951453.879943, 'stop': 1685951454.664951, '$report_type': 'TestReport', 'item_index': 577, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_relocate.py::test_relocate_symlinks', 'location': ('tests/test_relocate.py', 57, 'test_relocate_symlinks'), 'keywords': {'test_relocate_symlinks': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "bar": {\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo",\n "basename": "foo",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2/foo"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\ntotal 0\nlrwxr-xr-x 1 jasperk wheel 46 Jun 5 09:50 dir2 -> /Users/jasperk/gitlab/cwltool/tests/reloc/dir2\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job test.cwl] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmphfn_s4u0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl",\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job test.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/reloc/test.cwl\nDEBUG cwltool:command_line_tool.py:988 [job test.cwl] {\n "inp": {\n "class": "Directory",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "basename": "dir2"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job test.cwl] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job test.cwl] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job test.cwl] initial work dir {\n "file:///Users/jasperk/gitlab/cwltool/tests/reloc/dir2": [\n "/Users/jasperk/gitlab/cwltool/tests/reloc/dir2",\n "/private/tmp/docker_tmphfn_s4u0/dir2",\n "Directory",\n true\n ]\n}\nINFO cwltool:job.py:266 [job test.cwl] /private/tmp/docker_tmphfn_s4u0$ ls \\\n -l\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job test.cwl] completed success\nDEBUG cwltool:job.py:422 [job test.cwl] outputs {\n "bar": {\n "location": "file:///private/tmp/docker_tmphfn_s4u0/dir2/foo",\n "basename": "foo",\n "nameroot": "foo",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job test.cwl] Removing input staging directory /private/tmp/docker_tmp0juuwyi8\nDEBUG cwltool:job.py:454 [job test.cwl] Removing temporary directory /private/tmp/docker_tmpd73wvlsx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmphfn_s4u0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007529229997089715, 'start': 1685951454.666344, 'stop': 1685951454.667098, '$report_type': 'TestReport', 'item_index': 577, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_relocate.py::test_relocate_symlinks - location: ('tests/test_relocate.py', 57, 'test_relocate_symlinks') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_schemadef.py::test_schemadef - location: ('tests/test_schemadef.py', 7, 'test_schemadef') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_schemadef.py::test_schemadef', 'location': ('tests/test_schemadef.py', 7, 'test_schemadef'), 'keywords': {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00033530900054756785, 'start': 1685951454.669056, 'stop': 1685951454.6693928, '$report_type': 'TestReport', 'item_index': 578, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\uadf8\\ub798\\ud504]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]'), 'keywords': {'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\uadf8\\ub798\\ud504': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "path": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "dirname": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmpcqcthnlx$ cat \\\n /private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/그래프 > /private/tmp/docker_tmpcqcthnlx/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpcqcthnlx/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing input staging directory /private/tmp/docker_tmpmcy_zp2s\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] Removing temporary directory /private/tmp/docker_tmpfyrojqm7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpcqcthnlx/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpcqcthnlx\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "path": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "dirname": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmpcqcthnlx$ cat \\\n /private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/그래프 > /private/tmp/docker_tmpcqcthnlx/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpcqcthnlx/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpmcy_zp2s\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmpfyrojqm7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpcqcthnlx/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcqcthnlx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7386569559994314, 'start': 1685951454.106852, 'stop': 1685951454.845493, '$report_type': 'TestReport', 'item_index': 498, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 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"/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "dirname": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] /private/tmp/docker_tmpcqcthnlx$ cat \\\n /private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/그래프 > /private/tmp/docker_tmpcqcthnlx/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpcqcthnlx/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n 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cwltool:command_line_tool.py:982 [job script_2] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/script\nDEBUG cwltool:command_line_tool.py:988 [job script_2] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/\\uadf8\\ub798\\ud504",\n "size": 0,\n "basename": "\\uadf8\\ub798\\ud504",\n "nameroot": "\\uadf8\\ub798\\ud504",\n "nameext": "",\n "path": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/\\uadf8\\ub798\\ud504",\n "dirname": "/private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_2] initial work dir {}\nINFO cwltool:job.py:266 [job script_2] /private/tmp/docker_tmpcqcthnlx$ cat \\\n /private/tmp/docker_tmpmcy_zp2s/stg5479f823-b865-4c2a-a1ca-d42af62f8782/그래프 > /private/tmp/docker_tmpcqcthnlx/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_2] completed success\nDEBUG cwltool:job.py:422 [job script_2] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpcqcthnlx/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_2] Removing input staging directory /private/tmp/docker_tmpmcy_zp2s\nDEBUG cwltool:job.py:454 [job script_2] Removing temporary directory /private/tmp/docker_tmpfyrojqm7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpcqcthnlx/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u1/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcqcthnlx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006455060001826496, 'start': 1685951454.846982, 'stop': 1685951454.847629, '$report_type': 'TestReport', 'item_index': 498, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\uadf8\ub798\ud504] - location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\uadf8\\ub798\\ud504]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u0433\u0440\u0430\u0444\u0438\u043a] - location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]'), 'keywords': {'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0025021310002557584, 'start': 1685951454.8497221, 'stop': 1685951454.852226, '$report_type': 'TestReport', 'item_index': 499, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]'), 'keywords': {'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "path": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "dirname": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmpvbrqfcce$ cat \\\n /private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/график > /private/tmp/docker_tmpvbrqfcce/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvbrqfcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmps8z5vcf7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmpmxdb7u8w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpvbrqfcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvbrqfcce\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "path": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "dirname": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmpvbrqfcce$ cat \\\n /private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/график > /private/tmp/docker_tmpvbrqfcce/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvbrqfcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmps8z5vcf7\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmpmxdb7u8w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvbrqfcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvbrqfcce\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6572173209997345, 'start': 1685951454.852916, 'stop': 1685951455.510119, '$report_type': 'TestReport', 'item_index': 499, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]'), 'keywords': {'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "path": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "dirname": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] /private/tmp/docker_tmpvbrqfcce$ cat \\\n /private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/график > /private/tmp/docker_tmpvbrqfcce/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_3] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvbrqfcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing input staging directory /private/tmp/docker_tmps8z5vcf7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_3] Removing temporary directory /private/tmp/docker_tmpmxdb7u8w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpvbrqfcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvbrqfcce\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_3] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/script\nDEBUG cwltool:command_line_tool.py:988 [job script_3] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "size": 0,\n "basename": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameroot": "\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "nameext": "",\n "path": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a",\n "dirname": "/private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_3] initial work dir {}\nINFO cwltool:job.py:266 [job script_3] /private/tmp/docker_tmpvbrqfcce$ cat \\\n /private/tmp/docker_tmps8z5vcf7/stg346ac9ec-a370-40f0-99e2-be8d933b03fd/график > /private/tmp/docker_tmpvbrqfcce/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_3] completed success\nDEBUG cwltool:job.py:422 [job script_3] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvbrqfcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_3] Removing input staging directory /private/tmp/docker_tmps8z5vcf7\nDEBUG cwltool:job.py:454 [job script_3] Removing temporary directory /private/tmp/docker_tmpmxdb7u8w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvbrqfcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u2/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvbrqfcce\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005697329997929046, 'start': 1685951455.511276, 'stop': 1685951455.511847, '$report_type': 'TestReport', 'item_index': 499, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u0433\u0440\u0430\u0444\u0438\u043a] - location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0433\\u0440\\u0430\\u0444\\u0438\\u043a]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\U00012043] - location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\U00012043]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\U00012043]'), 'keywords': {'test_unicode_in_input_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001521131000117748, 'start': 1685951455.513267, 'stop': 1685951455.514789, '$report_type': 'TestReport', 'item_index': 500, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\U00012043]'), 'keywords': {'test_unicode_in_input_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "path": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "dirname": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmp3zambcce$ cat \\\n /private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/ð’ƒ > /private/tmp/docker_tmp3zambcce/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp3zambcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmp2gyrl7es\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmplnp87_ml\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp3zambcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp3zambcce\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "path": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "dirname": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmp3zambcce$ cat \\\n /private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/ð’ƒ > /private/tmp/docker_tmp3zambcce/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp3zambcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmp2gyrl7es\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmplnp87_ml\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp3zambcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3zambcce\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6731989129993963, 'start': 1685951455.515143, 'stop': 1685951456.188326, '$report_type': 'TestReport', 'item_index': 500, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\U00012043]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\U00012043]'), 'keywords': {'test_unicode_in_input_files[\\U00012043]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\U00012043': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "path": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "dirname": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] /private/tmp/docker_tmp3zambcce$ cat \\\n /private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/ð’ƒ > /private/tmp/docker_tmp3zambcce/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_4] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp3zambcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing input staging directory /private/tmp/docker_tmp2gyrl7es\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_4] Removing temporary directory /private/tmp/docker_tmplnp87_ml\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp3zambcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp3zambcce\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_4] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/script\nDEBUG cwltool:command_line_tool.py:988 [job script_4] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_4] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/\\ud808\\udc43",\n "size": 0,\n "basename": "\\ud808\\udc43",\n "nameroot": "\\ud808\\udc43",\n "nameext": "",\n "path": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/\\ud808\\udc43",\n "dirname": "/private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_4] initial work dir {}\nINFO cwltool:job.py:266 [job script_4] /private/tmp/docker_tmp3zambcce$ cat \\\n /private/tmp/docker_tmp2gyrl7es/stg44dbc8d4-3382-4b1a-bffa-8f96f5c71c8b/ð’ƒ > /private/tmp/docker_tmp3zambcce/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_4] completed success\nDEBUG cwltool:job.py:422 [job script_4] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp3zambcce/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_4] Removing input staging directory /private/tmp/docker_tmp2gyrl7es\nDEBUG cwltool:job.py:454 [job script_4] Removing temporary directory /private/tmp/docker_tmplnp87_ml\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp3zambcce/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__U3/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp3zambcce\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005871860003026086, 'start': 1685951456.189573, 'stop': 1685951456.190162, '$report_type': 'TestReport', 'item_index': 500, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\U00012043] - location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\U00012043]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u2615\U0001f60d] - location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u2615\\U0001f60d]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_input_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015364820001195767, 'start': 1685951456.1915379, 'stop': 1685951456.193076, '$report_type': 'TestReport', 'item_index': 501, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow', 'location': ('tests/test_provenance.py', 169, 'test_directory_workflow'), 'keywords': {'test_directory_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "dir1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": 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"/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0\ntest_directory_workflow0/\n cwltool-run/\n 9da56764e3939493b1b27e23e1a15413ad3c7789\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir2/\n a\n c\n b\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3ca69e8d6c234a469d16ac28a4a658c92267c423\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n metadata/\n directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n manifest.json\n directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n logs/\n engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp9k6tej38/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\n\x1b[1;30mINFO\x1b[0m [workflow _18] start\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmpkt9xn476$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpkt9xn476,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp5bdr87x6,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpijlt4w41/20230605095053-735575.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/ZYBRaV\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpu2ojz1u2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpu2ojz1u2,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1tlylhil,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2,target=/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2,readonly \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpl041cwt9/20230605095054-807591.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2 > /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 042ddf8c8e3a821bd2b1e0b31a7e999d8b6358cf workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 24bbc4fbeba486e56a28be585526c2bfea369513cfd06abeeae6f38289755031 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: adc92e3ab02558f989f144b96d6ff9faf8db91d319f1611c703cb2aaf05062ff6c88fa7376128236b98ba553c2f4e51d88a9cf878fb25a435b907b96318c87f5 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp9k6tej38/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\', \'basename\': \'dir2\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\', \'basename\': \'dir2\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e2a2c4c0c09ac506044b76ffa3081669e50a8ff3 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: d8a50ec3ed7c9940992d5d94ad6f81fe7939d212e7e4267d8999537ea4c1f646 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 3b93050d00a41067c2b8308f1513c3f4c66f1d61d0255c926adb5a4676e5a4174c1764345be25ec811c6c9011799d8427b5f2a9865ee167e4cdd4dd6a30d24f8 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 65d233a8c5869bfb70c5a96f3ccca98fc755c3cd metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 9e0308c4e8c8b0510143d7bc960cfbc97d913a436f42304fb901bf90703192af metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 2ab14b39b928bae6b37bc1b9768a16e683c7b90f7ba46f7fe8c137e1264de2a40e06bfa24120beb97dab2b6fa013ac518d12fcda42bb0f950b8bdf052c1f7107 metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#generate/23607ac8-6d07-4c00-9c5b-47c558e7e9e3 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmpkt9xn476$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpkt9xn476,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp5bdr87x6,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpijlt4w41/20230605095053-735575.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 198893dacc70f008f36bbba2fe29d8535c5bd23c metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 120d87f124da54fd9a263778a81bda3cf1a045665303d8422d7d027a264a647d metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: cf443274e5daf84d8ac240b69e536f9a8017420be7388845de2a8a12a3b31e0500a5e17aae827602fa5214ebb387d8dc1f334530a1fff49734bedeb9185376eb metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 1c8ccffbd02455f5b16a28836157c37edbbd7d77 metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2795901e7f86ddfde453d6c6f4c515b4608f02afb0ffebc217f6d1f76e75fa1f metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 4183293ca0948a62bc5609c8e687c58f2aebb5015a693acfe4a0c84c3fdacbbd46b22d44e94bafeee94e4e1e59dc929cde5fec0f467f623ece8617810445f5ba metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 391eeef64e45451497068dd5e08da5526dc09261 metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 1290f6ee522ff20dfbe311c166e239a66b2695d4cf472ac22ca913b4b8982aa2 metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: a06e1c046bd187d30da601ee5230847ca50e3cd4722f7274033f9fa42f3b359600fa6b78271b80b84927d05b677756afecd891546c105373a7a2d13db9ae38ef metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmp_hi49kn9\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmp5bdr87x6\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/fa09414f-ed1d-4d5f-b17c-ca711545c8f7 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1,\n "nameroot": "a",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1,\n "nameroot": "c",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1,\n "nameroot": "b",\n "nameext": ""\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/b",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1,\n "nameroot": "a",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/a",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1,\n "nameroot": "c",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/c",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1,\n "nameroot": "b",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/b",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n }\n ],\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpu2ojz1u2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpu2ojz1u2,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1tlylhil,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2,target=/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2,readonly \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpl041cwt9/20230605095054-807591.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2 > /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e39ed4a096a3838fe29476728ed1690251cf9fcc metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: b4d7377020d3c1537390509ee07c720ebc847dd48dd479f81e4d76135e2c1f5e metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 483139b37ee1298386820473b14d45c1e81c2454a88959901a5f316639222493a366006aae408898a12fb905c2ad6c635a62f114ad9b7346d5a4a330556e4c31 metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 3ca69e8d6c234a469d16ac28a4a658c92267c423 data/3c/3ca69e8d6c234a469d16ac28a4a658c92267c423\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3ca69e8d6c234a469d16ac28a4a658c92267c423\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n },\n "listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmp2nij54vg\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmp1tlylhil\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpkt9xn476/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe9xc_cpt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu2ojz1u2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkt9xn476\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: c9a6048adf16b96a3869b9d12b8286e0515ae36d metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 939d58de0735b845eeefa4ba7f1c76645eec447303f3b2ae7fab39a9141e6fad metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 6aa596c047b207982f4869bad52eef0dea77db8d82fd9171992d01945bbfbd80800e76ea7018b8bbf86919beef12dcd52dd079a1a7b0705f35f5fc98fd678b21 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 3ac9d7e8c8910108a2ac2f19e44c0e1cf0763451 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 117c9848067265d8ef2fce02241d8e9774f7bca2d12a178683d4827b05478e43 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 493868b27cf007925a3e58ef2cd98597bdd9b0f4e6862644141f079556a33caae08808f96cb8787481cfad9f099ff9562d86c5e8a984eab1c6ed1807d0a76370 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 42c0f1a3661c458606a81f1b63e1b366ca5ed3b5 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 8f2303580e0ce0716d6f0155046cd0e94d484e6524dfded385050b48c300b793 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 48dab132f2cdb691e06380f74c2f7accd0081881124e50c4f38f08cf82e55c231c1611e05cb6f592d97496a13657b96d245c54350d167193fb1b5b9b90f76daf metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 05620a0dfaf1b2d665632f07125d47e98f7df122 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 4f287deb230de31c0d0591206b5e62ef5c8f6ebe124ff22de3fb5a8893bb60e8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 9ade5e90f3c98bc847d54ef557dbee2fb1f12754778362cab0fcf977f70b1f0361e7781fbf117677ade07392a9b69171e755c4636a8ad1ad4f9e2da93d908ef1 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 3199ddc82637a20ecd91da0406042cc741021f2e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 3c8cafd4b517f67bb0fc00cb5e9d75326550804914149c0ca358c59e41ed3d51 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: d39410eb9650f5fcfbfddd101b10bb2dfc717452c2d3e985fdb45b049981151066c8c71f3231b4b69984226f18f2ef72abae04f81ac0448d173fb5728d5b83f5 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: c5ff5ff5b641194487ba00f3df5dd132661fb71a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2f6ebea0ad7601b5fa4ecb3e71edd28daa82f4478ab040ec5c0ee62731cd0eb2 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 12e7b62224e7e8549380e61043b28f6f7a92c047152369eade1d78f53c8cce91e5c734e0a919472e09aaba18c226a2d8052da297eeff5f67b8c17c5335072dc6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': 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[{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}], \'@id\': \'urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}], \'@id\': \'urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': 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\'urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 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\'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 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Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789\', \'basename\': \'9da56764e3939493b1b27e23e1a15413ad3c7789\', \'nameroot\': \'9da56764e3939493b1b27e23e1a15413ad3c7789\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/3c/3ca69e8d6c234a469d16ac28a4a658c92267c423\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 6\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 1013708c64fb5c51c7ebc74b8a834426cecf9a1f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: f59e18308696286011eb93b7d4f5acf7fb95268e205ced5010e8de2e2a7fb76b workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 77fba2e4a27d69e9eb78969d2ce5fa419d303828fa45f2974e79d9d555e68124cf8277aa7c3a773523b5f9afe4b2431d62ecb49d759cbdcc453514c01454805d workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 5c190af3abd6079fe9da0468818cef0894181ac3 snapshot/directory.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: b2e92881035af88a19765af7e9df298b4016ef43abdd8cde2768230494a6d561 snapshot/directory.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 8803193308dc28ac67e1d538bba1654a7a360e78bf25e71033c277a87f2f10a2643ee86d8cdf73725b7d1021110751f7bc4af4837e95a744d0c37611b09d5552 snapshot/directory.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: bbe97be74e01f68cd004fc10e9b02bde62d75506 metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 5b9a62b72e37e113bcde38bffb56be6551e0173693001915cd9bad0e7d74c6cd metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: a6fc64310c8dafcb54e539e6f25e029bfa7722635d44fbafe52953076fa619c3ae9276c15ad028811e98548096f4b5ae2f0758ae5602c17ba24acd7699fb550a metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e2524a4c4ca0e522cca2b37509d06ea46b20365e metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2f614db0992a28531588c3257650bf7245545bc4f2d5ab971a60f4ed00a01212 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 8f9eefc548aa7137857158666d7d7eceb74f525c8f452b5b5abe433b0e93de184c39397edea61b4e9f99aff6ab5a914f2aaa97b7420efba246e69b8dcf97e575 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: bde438d394d945f9c887bddad2ad0d8162a3af1c bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 454398ea0e8117e9932d5369afd1eb094744c0d157ff620f57b3b965fe65d515 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 197441240163d2867acacff0eab70980a9db59aaaef3d4736472436086ebc064478520bf7917ef56f3fb2c165bcd3d847ca9d23bda182d56fbeffd5125c5edc7 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance')], 'duration': 5.3208884470004705, 'start': 1685951451.105163, 'stop': 1685951456.425921, '$report_type': 'TestReport', 'item_index': 531, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow', 'location': ('tests/test_provenance.py', 169, 'test_directory_workflow'), 'keywords': {'test_directory_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "dir1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1"\n },\n "listing": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0\ntest_directory_workflow0/\n cwltool-run/\n 9da56764e3939493b1b27e23e1a15413ad3c7789\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir2/\n a\n c\n b\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3ca69e8d6c234a469d16ac28a4a658c92267c423\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n metadata/\n directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n manifest.json\n directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n logs/\n engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp9k6tej38/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\n\x1b[1;30mINFO\x1b[0m [workflow _18] start\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmpkt9xn476$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpkt9xn476,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp5bdr87x6,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpijlt4w41/20230605095053-735575.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/ZYBRaV\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpu2ojz1u2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpu2ojz1u2,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1tlylhil,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2,target=/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2,readonly \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpl041cwt9/20230605095054-807591.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2 > /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 042ddf8c8e3a821bd2b1e0b31a7e999d8b6358cf workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 24bbc4fbeba486e56a28be585526c2bfea369513cfd06abeeae6f38289755031 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: adc92e3ab02558f989f144b96d6ff9faf8db91d319f1611c703cb2aaf05062ff6c88fa7376128236b98ba553c2f4e51d88a9cf878fb25a435b907b96318c87f5 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp9k6tej38/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\', \'basename\': \'dir2\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2\', \'basename\': \'dir2\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir2\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\', \'basename\': \'a\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\', \'basename\': \'c\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\', \'basename\': \'b\', \'size\': 1}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e2a2c4c0c09ac506044b76ffa3081669e50a8ff3 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: d8a50ec3ed7c9940992d5d94ad6f81fe7939d212e7e4267d8999537ea4c1f646 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 3b93050d00a41067c2b8308f1513c3f4c66f1d61d0255c926adb5a4676e5a4174c1764345be25ec811c6c9011799d8427b5f2a9865ee167e4cdd4dd6a30d24f8 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 65d233a8c5869bfb70c5a96f3ccca98fc755c3cd metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 9e0308c4e8c8b0510143d7bc960cfbc97d913a436f42304fb901bf90703192af metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 2ab14b39b928bae6b37bc1b9768a16e683c7b90f7ba46f7fe8c137e1264de2a40e06bfa24120beb97dab2b6fa013ac518d12fcda42bb0f950b8bdf052c1f7107 metadata/directory-b5c2c6b9-8068-43be-a434-528a785b8d68.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#generate/23607ac8-6d07-4c00-9c5b-47c558e7e9e3 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmpkt9xn476$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpkt9xn476,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp5bdr87x6,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpijlt4w41/20230605095053-735575.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 198893dacc70f008f36bbba2fe29d8535c5bd23c metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 120d87f124da54fd9a263778a81bda3cf1a045665303d8422d7d027a264a647d metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: cf443274e5daf84d8ac240b69e536f9a8017420be7388845de2a8a12a3b31e0500a5e17aae827602fa5214ebb387d8dc1f334530a1fff49734bedeb9185376eb metadata/directory-a09b0d27-48f3-4b2d-967b-4f47c5687460.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 1c8ccffbd02455f5b16a28836157c37edbbd7d77 metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2795901e7f86ddfde453d6c6f4c515b4608f02afb0ffebc217f6d1f76e75fa1f metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 4183293ca0948a62bc5609c8e687c58f2aebb5015a693acfe4a0c84c3fdacbbd46b22d44e94bafeee94e4e1e59dc929cde5fec0f467f623ece8617810445f5ba metadata/directory-58761eba-559e-4065-bcdf-9c3758f25400.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 391eeef64e45451497068dd5e08da5526dc09261 metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 1290f6ee522ff20dfbe311c166e239a66b2695d4cf472ac22ca913b4b8982aa2 metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: a06e1c046bd187d30da601ee5230847ca50e3cd4722f7274033f9fa42f3b359600fa6b78271b80b84927d05b677756afecd891546c105373a7a2d13db9ae38ef metadata/directory-596a8455-3d93-4330-b12e-95d7e7419985.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmp_hi49kn9\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmp5bdr87x6\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/fa09414f-ed1d-4d5f-b17c-ca711545c8f7 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1,\n "nameroot": "a",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1,\n "nameroot": "c",\n "nameext": ""\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1,\n "nameroot": "b",\n "nameext": ""\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/b",\n "File",\n false\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2",\n "basename": "dir2",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/a",\n "basename": "a",\n "size": 1,\n "nameroot": "a",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/a",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/c",\n "basename": "c",\n "size": 1,\n "nameroot": "c",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/c",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2/b",\n "basename": "b",\n "size": 1,\n "nameroot": "b",\n "nameext": "",\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2/b",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2"\n }\n ],\n "path": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2",\n "dirname": "/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpu2ojz1u2$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpu2ojz1u2,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1tlylhil,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/dir2,target=/var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2,readonly \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpl041cwt9/20230605095054-807591.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stg3425fd82-5c23-42b9-b79f-9dd887027c1f/dir2 > /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e39ed4a096a3838fe29476728ed1690251cf9fcc metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: b4d7377020d3c1537390509ee07c720ebc847dd48dd479f81e4d76135e2c1f5e metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 483139b37ee1298386820473b14d45c1e81c2454a88959901a5f316639222493a366006aae408898a12fb905c2ad6c635a62f114ad9b7346d5a4a330556e4c31 metadata/directory-c201884c-09a9-4ae0-8134-21201f15eca7.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/manifest-sha1.txt: 3ca69e8d6c234a469d16ac28a4a658c92267c423 data/3c/3ca69e8d6c234a469d16ac28a4a658c92267c423\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir2\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3ca69e8d6c234a469d16ac28a4a658c92267c423\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969"\n }\n ],\n "@id": "urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460"\n }\n ],\n "@id": "urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmpkt9xn476/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8"\n }\n ]\n },\n "listing": {\n "location": "file:///private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789",\n "basename": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameroot": "9da56764e3939493b1b27e23e1a15413ad3c7789",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423",\n "size": 6,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954"\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmp2nij54vg\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmp1tlylhil\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpkt9xn476/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpu2ojz1u2/9da56764e3939493b1b27e23e1a15413ad3c7789 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe9xc_cpt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpu2ojz1u2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkt9xn476\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: c9a6048adf16b96a3869b9d12b8286e0515ae36d metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 939d58de0735b845eeefa4ba7f1c76645eec447303f3b2ae7fab39a9141e6fad metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 6aa596c047b207982f4869bad52eef0dea77db8d82fd9171992d01945bbfbd80800e76ea7018b8bbf86919beef12dcd52dd079a1a7b0705f35f5fc98fd678b21 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 3ac9d7e8c8910108a2ac2f19e44c0e1cf0763451 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 117c9848067265d8ef2fce02241d8e9774f7bca2d12a178683d4827b05478e43 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 493868b27cf007925a3e58ef2cd98597bdd9b0f4e6862644141f079556a33caae08808f96cb8787481cfad9f099ff9562d86c5e8a984eab1c6ed1807d0a76370 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 42c0f1a3661c458606a81f1b63e1b366ca5ed3b5 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 8f2303580e0ce0716d6f0155046cd0e94d484e6524dfded385050b48c300b793 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 48dab132f2cdb691e06380f74c2f7accd0081881124e50c4f38f08cf82e55c231c1611e05cb6f592d97496a13657b96d245c54350d167193fb1b5b9b90f76daf metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 05620a0dfaf1b2d665632f07125d47e98f7df122 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 4f287deb230de31c0d0591206b5e62ef5c8f6ebe124ff22de3fb5a8893bb60e8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 9ade5e90f3c98bc847d54ef557dbee2fb1f12754778362cab0fcf977f70b1f0361e7781fbf117677ade07392a9b69171e755c4636a8ad1ad4f9e2da93d908ef1 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 3199ddc82637a20ecd91da0406042cc741021f2e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 3c8cafd4b517f67bb0fc00cb5e9d75326550804914149c0ca358c59e41ed3d51 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: d39410eb9650f5fcfbfddd101b10bb2dfc717452c2d3e985fdb45b049981151066c8c71f3231b4b69984226f18f2ef72abae04f81ac0448d173fb5728d5b83f5 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: c5ff5ff5b641194487ba00f3df5dd132661fb71a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2f6ebea0ad7601b5fa4ecb3e71edd28daa82f4478ab040ec5c0ee62731cd0eb2 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 12e7b62224e7e8549380e61043b28f6f7a92c047152369eade1d78f53c8cce91e5c734e0a919472e09aaba18c226a2d8052da297eeff5f67b8c17c5335072dc6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}], \'@id\': \'urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\'}]}, \'listing\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789\', \'basename\': \'9da56764e3939493b1b27e23e1a15413ad3c7789\', \'nameroot\': \'9da56764e3939493b1b27e23e1a15413ad3c7789\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}], \'@id\': \'urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:596a8455-3d93-4330-b12e-95d7e7419985\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}], \'@id\': \'urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}], \'@id\': \'urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0a903e94-0cb7-4026-974e-6dfa68663e99\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}], \'@id\': \'urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:208ecd52-ee98-4553-8d32-f5f608930969\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a09b0d27-48f3-4b2d-967b-4f47c5687460\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:58761eba-559e-4065-bcdf-9c3758f25400\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:088d5f5c-1aca-4f04-b9ba-087ae90bd0d8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/cwltool-run/9da56764e3939493b1b27e23e1a15413ad3c7789\', \'basename\': \'9da56764e3939493b1b27e23e1a15413ad3c7789\', \'nameroot\': \'9da56764e3939493b1b27e23e1a15413ad3c7789\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423\', \'size\': 6, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/3c/3ca69e8d6c234a469d16ac28a4a658c92267c423\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 9da56764e3939493b1b27e23e1a15413ad3c7789\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$3ca69e8d6c234a469d16ac28a4a658c92267c423\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 6\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a0286b39-8a65-4aa5-8862-9cf3cffb1954\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 1013708c64fb5c51c7ebc74b8a834426cecf9a1f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: f59e18308696286011eb93b7d4f5acf7fb95268e205ced5010e8de2e2a7fb76b workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 77fba2e4a27d69e9eb78969d2ce5fa419d303828fa45f2974e79d9d555e68124cf8277aa7c3a773523b5f9afe4b2431d62ecb49d759cbdcc453514c01454805d workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: 5c190af3abd6079fe9da0468818cef0894181ac3 snapshot/directory.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: b2e92881035af88a19765af7e9df298b4016ef43abdd8cde2768230494a6d561 snapshot/directory.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 8803193308dc28ac67e1d538bba1654a7a360e78bf25e71033c277a87f2f10a2643ee86d8cdf73725b7d1021110751f7bc4af4837e95a744d0c37611b09d5552 snapshot/directory.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: bbe97be74e01f68cd004fc10e9b02bde62d75506 metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 5b9a62b72e37e113bcde38bffb56be6551e0173693001915cd9bad0e7d74c6cd metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: a6fc64310c8dafcb54e539e6f25e029bfa7722635d44fbafe52953076fa619c3ae9276c15ad028811e98548096f4b5ae2f0758ae5602c17ba24acd7699fb550a metadata/logs/engine.c5e239e6-4793-49c2-a275-f05688d3e9de.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: e2524a4c4ca0e522cca2b37509d06ea46b20365e metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 2f614db0992a28531588c3257650bf7245545bc4f2d5ab971a60f4ed00a01212 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 8f9eefc548aa7137857158666d7d7eceb74f525c8f452b5b5abe433b0e93de184c39397edea61b4e9f99aff6ab5a914f2aaa97b7420efba246e69b8dcf97e575 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha1.txt: bde438d394d945f9c887bddad2ad0d8162a3af1c bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha256.txt: 454398ea0e8117e9932d5369afd1eb094744c0d157ff620f57b3b965fe65d515 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b/tagmanifest-sha512.txt: 197441240163d2867acacff0eab70980a9db59aaaef3d4736472436086ebc064478520bf7917ef56f3fb2c165bcd3d847ca9d23bda182d56fbeffd5125c5edc7 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tjhjd41b\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_directory_workflow0/provenance')], 'duration': 0.0009654089999457938, 'start': 1685951456.42858, 'stop': 1685951456.4295459, '$report_type': 'TestReport', 'item_index': 531, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_directory_workflow - location: ('tests/test_provenance.py', 169, 'test_directory_workflow') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - when: runtest - nodeid: tests/test_provenance.py::test_directory_workflow - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_no_data_files - location: ('tests/test_provenance.py', 211, 'test_no_data_files') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_no_data_files', 'location': ('tests/test_provenance.py', 211, 'test_no_data_files'), 'keywords': {'test_no_data_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012377330003801035, 'start': 1685951456.4334888, 'stop': 1685951456.434727, '$report_type': 'TestReport', 'item_index': 532, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_input_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "path": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "dirname": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmp_61iiwhz$ cat \\\n /private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/☕😠> /private/tmp/docker_tmp_61iiwhz/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_61iiwhz/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpx9yowb6j\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpyb8f0uu7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp_61iiwhz/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp_61iiwhz\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "path": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "dirname": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmp_61iiwhz$ cat \\\n /private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/☕😠> /private/tmp/docker_tmp_61iiwhz/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_61iiwhz/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpx9yowb6j\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpyb8f0uu7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_61iiwhz/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_61iiwhz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7255514700000276, 'start': 1685951456.1934872, 'stop': 1685951456.919023, '$report_type': 'TestReport', 'item_index': 501, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u2615\\U0001f60d]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u2615\\U0001f60d]'), 'keywords': {'test_unicode_in_input_files[\\u2615\\U0001f60d]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u2615\\U0001f60d': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "path": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "dirname": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] /private/tmp/docker_tmp_61iiwhz$ cat \\\n /private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/☕😠> /private/tmp/docker_tmp_61iiwhz/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_61iiwhz/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing input staging directory /private/tmp/docker_tmpx9yowb6j\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_5] Removing temporary directory /private/tmp/docker_tmpyb8f0uu7\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp_61iiwhz/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp_61iiwhz\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_5] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/script\nDEBUG cwltool:command_line_tool.py:988 [job script_5] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_5] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_5] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/\\u2615\\ud83d\\ude0d",\n "size": 0,\n "basename": "\\u2615\\ud83d\\ude0d",\n "nameroot": "\\u2615\\ud83d\\ude0d",\n "nameext": "",\n "path": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/\\u2615\\ud83d\\ude0d",\n "dirname": "/private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_5] initial work dir {}\nINFO cwltool:job.py:266 [job script_5] /private/tmp/docker_tmp_61iiwhz$ cat \\\n /private/tmp/docker_tmpx9yowb6j/stga5eb1bbe-4585-4bf8-bbd3-6f978773c1dd/☕😠> /private/tmp/docker_tmp_61iiwhz/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_5] completed success\nDEBUG cwltool:job.py:422 [job script_5] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_61iiwhz/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_5] Removing input staging directory /private/tmp/docker_tmpx9yowb6j\nDEBUG cwltool:job.py:454 [job script_5] Removing temporary directory /private/tmp/docker_tmpyb8f0uu7\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_61iiwhz/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u4/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_61iiwhz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008311599995067809, 'start': 1685951456.9203131, 'stop': 1685951456.9211478, '$report_type': 'TestReport', 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config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow_no_listing', 'location': ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing'), 'keywords': {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'failed', 'longrepr': {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 891, 'message': "AssertionError: assert not True\n + where True = ()\n + where = PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4').is_file"}, 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[('Captured stdout call', '{\n "output_1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad"\n },\n "output_2": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0\ntest_directory_workflow_no_lis0/\n cwltool-run/\n 511f5ede99eeae60df68dedf0f5a3c2886774dad\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir_no_info/\n f\n d\n e\n dir_deep_listing/\n a\n c\n b\n dir_no_listing/\n f\n d\n e\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory_no_listing.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3c363836cf4e16666669a25da280a1865c2d2874\n 58/\n 58e6b3a414a1e090dfc6029add0f3555ccba127f\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n a0/\n a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n 4a/\n 4a0a19218e082a343a1b17e5333409af9d98f0f5\n metadata/\n directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n manifest.json\n directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n logs/\n engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/KKDWnh\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'--ignore\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'--ignore_no_info\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: bf9a8c91a428be6becd92c778c02c67d427411a8 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f63ffc058c8cfdb908506337c548afa6df073ae4c60dfd126529041314a548a5 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4fd8262b0744c271fe42c0c7a3142522708348559d0e405bb03bf2ab6becbeb7f64fecd3d8fb0762aa478fd99791200d9c3503e2e2e47b16546bd96fda2bca33 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing"\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}, \'ignore\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}, \'ignore_no_info\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_deep_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_info\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: b8ccdd89c80eca48567812797b860122d330b485 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: c1d4042283d1ce80021fa05c18eed2ae1bffea933f49ddd960b4a09f9a262cb5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: bdc150fa3761c3d002efb9be43f71cf8dac2e1f42259fdff201f185d0603839f2b882baf2cf28656ecfdfa1519fdf92a6b8611fab87b17604c45c09e28ed72ee workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ba113d80556b23c15fd7c2455789b16fe31f2335 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9ae22ea23ca80ffebd84f7e8ff4b640ec2d0f1956c56555485252b0f43892ce6 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 2b38d01f508e3abb2d8249e19be4d222e1b13c37943489f70523fa076f09d012a4f139a3b480706cd411ec961a4f8dcb5b255404f7f71fa74a24bf1886f66889 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 4a0a19218e082a343a1b17e5333409af9d98f0f5 data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 3c363836cf4e16666669a25da280a1865c2d2874 data/3c/3c363836cf4e16666669a25da280a1865c2d2874\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 58e6b3a414a1e090dfc6029add0f3555ccba127f data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 2de598f6b273e2eaaabca9703f0ca739ac4fb4bd metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 803eefe7af4871fc1029330cf00afb4abc33e44591400b6036c887ce4d3516c8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 26f9234c3e7852c13da1a41405bba99f80817d45abf0beed442c3c31cd106afb3b4bdc96fced5ce6e84194af3d156b1c880cef95d9283e3a98f6a87af04e40b8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 94788d2e8451e82a089085ce9a13d21d7648a56a metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: be9b32c701e852c1cce196ed17bb7d04ce147cda1847a2bb31b81a0b3b3bdfb8 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 7f08203a26bde01dd72f0888a87167b6ac571b24e88928de1d73b3cdfcd873e5576f2ccb107b88fa663be20691607e6c74c57f73e2ab5acfa2da3ab1242a5465 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info",\n "basename": "dir_no_info"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from _:c64797b9-0e72-438b-b250-9a183c2486c6 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a01f4d65bf45da813bc5c1482c403b467537faba metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b68aeee0d249094334ad30ea74bf2e8e13de8620ffba8d87dd4ff03f4f707c9 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 0508e90f315884b3b5652850fe11970d60be330ecc6079e443b6f9cf8cdd539ccd6f0f679d05b0ee5c9da1550a3ca81b79425c9b07bca981a24338d10441f318 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 456e3bd591c3db18d15eb03f1b0033f71af12d3a metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 0b6bb416adfdfd452957e1ece6c05a5065835bb85234d7946a264c4016248028 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 856999b9b5ec46248fac41601440d838ba31b12e7c942005522d5e3ef91ebc7edd707457acdfc7d46895a185beb5785592c34d596e22cfb805edc527fc62a209 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9c22bec2e40d921fa850aa5fff207217b2700033 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f8c81c1297aa21b9e5e6d72fbdd4d5bb4dbc5fcc7a8332e4eb07cc6af6620171 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 59200606c8f78dec7b9c4ee540aa62a420c89b773788766589cc20849df29bc5ad624c61cd642b3eb214ab9d94598f99d290690e5e9668690398e7fee40211c3 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmpuu8p9qg8\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmpgouh1jdv\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from _:6798550b-35c6-4878-b539-969960c2ddd6 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "Directory",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n }\n ],\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f"\n }\n },\n {\n "position": [\n 2,\n "ignore"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing",\n "path": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "dirname": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 8cc5feedb2b21504d21859e0f63631f0b517553b metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b0f753abd9f52fa7bda09156130e6b0b936f1cd0705a6894db0eadff26b12a1 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: d6d5e13b344294994185ebcff17d42825d055b22a1e88978298377197522f2542db43987450874f4fd8da234a974070ce23ac03eff61c0a5a647d4c97a68cec6 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 18386d0fde6d11e92ff3eb4475f6553b3093c775 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 31c7501fcee1311e24b50b4142dc0321239dbdaaf821e84c7370321898b234d3 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: be3cf5fc2ba70daafbc4cfe1fe3dd41ee9772f0cccd8f955aa6b0c619abb9eda2bc00818090ad245ffe663fb8151f5b965feb7f4933e3ce68e7d38ff89aa3587 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: a0ce0441f957dcde10291470aa5062ffc7cbdf8c data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "output_1": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n },\n "output_2": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmphgdo2k_m\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmpy12k7j25\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp30294ykg/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe4wl6xjm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp30294ykg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp03q_qnzm\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 831d591ea563d82200f6b29cdbed89958af99946 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8591aab1f32872e19f186118be1462101272c003e5725780ad0a1053b4f45b8 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 1b73e532287cafb4438cfc69dd62ca998d374d25d2d2a9e1aae2d80da74193ec8abc5494227ed037b4a9cbcebd72b4ba2f5c5a995fc9406ad87abc08a421237a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 52917a96deb1331e4f3e0d0c0ca5c06da11b550f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 952621e5f975fa4b8536d1246e03019673efe29716be7dd946885b26420ad858 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 9d13a8b2e9919c7d90a5b65c0af7326c4869efebe2b1525d1dee1d573159349fa8c3d9a06386e6e3054b4517ac86f5389bb90d9cc8105857baa9a142a9958123 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 4660384a529ef8217263414cfe7d8e09a36dae6a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8d43e02f50436e6bc3d92fdf3f37d0452a90fb55cc177c4902b62802ce733b8 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: c3a8205627d56adebcf5e2221b0ce6adc18bebc2af049dbec6dd744c90d1d704cca928860c5b41a8c0fa7056484ca8a454555ab058b982a5a5b3c4b48e35de1d metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: de4b6608f9e3af201c70ff6b53f85749a8492405 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: fadae5349308a66d763eacbe40b6c0348bdfd6947a138a8f8adab6c451836db5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4eb4037e059930960700522093a233245189d1e1284b785d7642142d07ace00ecb89da2a98af756469be68dec3c3b6b0e41368ad4b0325b536fffb642fdc0280 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 153127a4ee5a028d1acd636b0809d434d53da02d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 717a4f8ae33902dcd217991e923892a59b626fe60f616d3cd275806d18e9da4a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 5c8ece230a9c9d65f0b953c27045f92d27e3d6ecc3823e7ef9d3cb4426d66ded6a1fddd45a4bfed846940ed9a1f4bc3f4e9159650a856e9c7bdde1a7162f4ead metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9a047fa31e52f7b66c1a7cebf88c57d9e388c8c6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: a727a73f4d563af8f90316d9ec809d0f853abc53632d2f306ca2944475293cdc metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 83f351fed5f621fa4763e6d0f0762964aa213f325926bf7c406e94eef34970695b9c599bfbd807565b497858edbdfbacc1c3001cbdfb54bb826e49da09ee004f metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'output_1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}, \'output_2\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': 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Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a259a2ddea0fb8dbe04ce95431c7b87d74444c8d workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f92dbdf72304f179e312894c469c59f4b08ddabf26264f1ad7a38aa6a527b39e workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 586e6634367c1f8cddf3f26d6e2c7ff826ce3677902c23890028d73f66b854b30eb013b70cecaefb3fdcb8f47fe266e7182f62f24b6f5d94973d73b7dbc04479 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 757937dc88f5d446a6e63c9d1f12acde32b02ecd snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 2c725914f45b19c49b5a6e9540477b70a0273cefdbd82c19de19054de16cb24f snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6d058c8a26fad02c7935f0ee249b186701f49d64ed43f8dccc87ca2f374356b971470006906e36f6d9c888cf50ead1e3fe3f6759e8d1d53a678ca6c1a171387a snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ec85041b357ff2b39338cfbc69d2560640966f89 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 36a504d2c4551667e228d84c4eed90bd73747fe98606b30d912ec9b1ec3767bd metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: f2e20d11de50af96dc8e3bfcd43f0bc8d78342dda00c88c80de92a8f04d4aa3bbf684bf7c59f342cb8ef84393e00327a65b1c107d18f4a449e6116496d5e1f54 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0033518ae68cb74ef1d56196451d0ac9957ce80f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 640cf34ac826eeba52a190d69e5d9f3e0cd8025e6c6a20a5c32c5a479c687c67 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6345ca41b6e0eedc5d3dc2a171ce96cb26aef6a6072f27634478eee2492ac756794ece6fd4949d827a922b55d0d2d7fd5c66b69ade15549c3b96aef4b86e9d0a metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0d2331dab4d408bceb1057cfe5f1e826e1990c29 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 37908e47bb9f9ca212410631fd36ca1f333b9640b281b15639bfc1a822730ba6 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 059ed78b311c6402fb86010caf6283f0bd799fc922264bbef8b82bfb774e14680d16ee89810d4a50f82511d03a2a7596afe8806d3137f4c749d9db1e3b533ca2 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance')], 'duration': 4.963674428999184, 'start': 1685951451.80366, 'stop': 1685951456.767212, '$report_type': 'TestReport', 'item_index': 570, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_directory_workflow_no_listing', 'location': ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing'), 'keywords': {'test_directory_workflow_no_listing': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output_1": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad"\n },\n "output_2": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1",\n "basename": "dir1",\n "class": "Directory",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt"\n },\n {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "size": 1,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1"\n }\n}Root: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0\ntest_directory_workflow_no_lis0/\n cwltool-run/\n 511f5ede99eeae60df68dedf0f5a3c2886774dad\n dir1/\n a.txt\n a/\n b.txt\n b/\n c.txt\n dir_no_info/\n f\n d\n e\n dir_deep_listing/\n a\n c\n b\n dir_no_listing/\n f\n d\n e\n provenance/\n bagit.txt\n bag-info.txt\n manifest-sha1.txt\n tagmanifest-sha256.txt\n tagmanifest-sha1.txt\n tagmanifest-sha512.txt\n snapshot/\n directory_no_listing.cwl\n workflow/\n packed.cwl\n primary-job.json\n primary-output.json\n data/\n 3c/\n 3c363836cf4e16666669a25da280a1865c2d2874\n 58/\n 58e6b3a414a1e090dfc6029add0f3555ccba127f\n 86/\n 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n a0/\n a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n e9/\n e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n 84/\n 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n 4a/\n 4a0a19218e082a343a1b17e5333409af9d98f0f5\n metadata/\n directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n manifest.json\n directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n logs/\n engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n provenance/\n primary.cwlprov.jsonld\n primary.cwlprov.json\n primary.cwlprov.xml\n primary.cwlprov.nt\n primary.cwlprov.ttl\n primary.cwlprov.provn\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\n\x1b[1;30mINFO\x1b[0m [workflow _17] start\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step generate\n\x1b[1;30mINFO\x1b[0m [step generate] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\n/KKDWnh\n\x1b[1;30mINFO\x1b[0m [job generate] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job generate] completed success\n\x1b[1;30mINFO\x1b[0m [step generate] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] starting step ls\n\x1b[1;30mINFO\x1b[0m [step ls] start\n\x1b[1;30mINFO\x1b[0m [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\n\x1b[1;30mINFO\x1b[0m [job ls] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job ls] completed success\n\x1b[1;30mINFO\x1b[0m [step ls] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _17] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl --dir /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing --ignore /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing --ignore_no_info /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\', job_order=[\'--dir\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'--ignore\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'--ignore_no_info\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: bf9a8c91a428be6becd92c778c02c67d427411a8 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f63ffc058c8cfdb908506337c548afa6df073ae4c60dfd126529041314a548a5 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4fd8262b0744c271fe42c0c7a3142522708348559d0e405bb03bf2ab6becbeb7f64fecd3d8fb0762aa478fd99791200d9c3503e2e2e47b16546bd96fda2bca33 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpz_42ldqz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl",\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing"\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'dir\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}, \'ignore\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}, \'ignore_no_info\': {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing\', \'basename\': \'dir_deep_listing\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_deep_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\', \'basename\': \'a\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 86f7e437faa5a7fce15d1ddcb9eaeaea377667b8 data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\', \'basename\': \'c\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 84a516841ba77a5b4648de2cd0dfcb30ea46dbb4 data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\', \'basename\': \'b\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98 data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing\', \'basename\': \'dir_no_listing\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_listing\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info\', \'basename\': \'dir_no_info\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: dir_no_info\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: b8ccdd89c80eca48567812797b860122d330b485 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: c1d4042283d1ce80021fa05c18eed2ae1bffea933f49ddd960b4a09f9a262cb5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: bdc150fa3761c3d002efb9be43f71cf8dac2e1f42259fdff201f185d0603839f2b882baf2cf28656ecfdfa1519fdf92a6b8611fab87b17604c45c09e28ed72ee workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ba113d80556b23c15fd7c2455789b16fe31f2335 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9ae22ea23ca80ffebd84f7e8ff4b640ec2d0f1956c56555485252b0f43892ce6 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 2b38d01f508e3abb2d8249e19be4d222e1b13c37943489f70523fa076f09d012a4f139a3b480706cd411ec961a4f8dcb5b255404f7f71fa74a24bf1886f66889 metadata/directory-33c737fb-143c-415a-829c-34696fae5466.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 4a0a19218e082a343a1b17e5333409af9d98f0f5 data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 3c363836cf4e16666669a25da280a1865c2d2874 data/3c/3c363836cf4e16666669a25da280a1865c2d2874\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: 58e6b3a414a1e090dfc6029add0f3555ccba127f data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 2de598f6b273e2eaaabca9703f0ca739ac4fb4bd metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 803eefe7af4871fc1029330cf00afb4abc33e44591400b6036c887ce4d3516c8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 26f9234c3e7852c13da1a41405bba99f80817d45abf0beed442c3c31cd106afb3b4bdc96fced5ce6e84194af3d156b1c880cef95d9283e3a98f6a87af04e40b8 metadata/directory-64a39c49-b322-439f-870a-ae5c21902781.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 94788d2e8451e82a089085ce9a13d21d7648a56a metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: be9b32c701e852c1cce196ed17bb7d04ce147cda1847a2bb31b81a0b3b3bdfb8 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 7f08203a26bde01dd72f0888a87167b6ac571b24e88928de1d73b3cdfcd873e5576f2ccb107b88fa663be20691607e6c74c57f73e2ab5acfa2da3ab1242a5465 metadata/directory-527b6bb2-31b7-4bbe-8e00-b396655600b6.ttl\n\nINFO cwltool:workflow_job.py:765 [workflow _17] start\nDEBUG cwltool:workflow_job.py:777 [workflow _17] inputs {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n },\n "ignore_no_info": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_info",\n "basename": "dir_no_info"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step generate\nDEBUG cwltool:workflow_job.py:727 [step generate] job input {}\nDEBUG cwltool:workflow_job.py:732 [step generate] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step generate] start\nDEBUG cwltool:command_line_tool.py:982 [job generate] initializing from _:c64797b9-0e72-438b-b250-9a183c2486c6 as part of step generate\nDEBUG cwltool:command_line_tool.py:988 [job generate] {}\nDEBUG cwltool:command_line_tool.py:1000 [job generate] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job generate] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job generate] initial work dir {}\nINFO cwltool:job.py:266 [job generate] /private/tmp/docker_tmp30294ykg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp30294ykg,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpgouh1jdv,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmphubg2lm0/20230605095054-375226.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n /bin/sh \\\n -c \\\n pwd; mkdir -p dir1/a/b; echo -n a > dir1/a.txt; echo -n b > dir1/a/b.txt; echo -n c > dir1/a/b/c.txt;\n\nINFO cwltool:job.py:905 [job generate] Max memory used: 0MiB\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a01f4d65bf45da813bc5c1482c403b467537faba metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b68aeee0d249094334ad30ea74bf2e8e13de8620ffba8d87dd4ff03f4f707c9 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 0508e90f315884b3b5652850fe11970d60be330ecc6079e443b6f9cf8cdd539ccd6f0f679d05b0ee5c9da1550a3ca81b79425c9b07bca981a24338d10441f318 metadata/directory-0f13fc0e-d432-4de8-8f20-b39d51151dd8.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 456e3bd591c3db18d15eb03f1b0033f71af12d3a metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 0b6bb416adfdfd452957e1ece6c05a5065835bb85234d7946a264c4016248028 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 856999b9b5ec46248fac41601440d838ba31b12e7c942005522d5e3ef91ebc7edd707457acdfc7d46895a185beb5785592c34d596e22cfb805edc527fc62a209 metadata/directory-a21c2d56-a76b-45d8-9a92-88ce71030a7b.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9c22bec2e40d921fa850aa5fff207217b2700033 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f8c81c1297aa21b9e5e6d72fbdd4d5bb4dbc5fcc7a8332e4eb07cc6af6620171 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 59200606c8f78dec7b9c4ee540aa62a420c89b773788766589cc20849df29bc5ad624c61cd642b3eb214ab9d94598f99d290690e5e9668690398e7fee40211c3 metadata/directory-31d13089-c645-4929-aefa-b2363e5de52b.ttl\n\nINFO cwltool:job.py:419 [job generate] completed success\nDEBUG cwltool:job.py:422 [job generate] outputs {\n "dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step generate] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#generate/dir1": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:572 [step generate] completed success\nDEBUG cwltool:job.py:446 [job generate] Removing input staging directory /private/tmp/docker_tmpuu8p9qg8\nDEBUG cwltool:job.py:454 [job generate] Removing temporary directory /private/tmp/docker_tmpgouh1jdv\nINFO cwltool:workflow_job.py:613 [workflow _17] starting step ls\nDEBUG cwltool:workflow_job.py:727 [step ls] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step ls] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b"\n }\n ]\n },\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nINFO cwltool:workflow_job.py:75 [step ls] start\nDEBUG cwltool:command_line_tool.py:982 [job ls] initializing from _:6798550b-35c6-4878-b539-969960c2ddd6 as part of step ls\nDEBUG cwltool:command_line_tool.py:988 [job ls] {\n "dir": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1\n }\n ]\n },\n "ignore": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job ls] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "Directory",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "File",\n false\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "Directory",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job ls] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n },\n {\n "position": [\n 1,\n "dir"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing",\n "basename": "dir_deep_listing",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/a",\n "basename": "a",\n "nameroot": "a",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/a",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/c",\n "basename": "c",\n "nameroot": "c",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/c",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n },\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing/b",\n "basename": "b",\n "nameroot": "b",\n "nameext": "",\n "size": 1,\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing/b",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing"\n }\n ],\n "path": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing",\n "dirname": "/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f"\n }\n },\n {\n "position": [\n 2,\n "ignore"\n ],\n "datum": {\n "class": "Directory",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing",\n "basename": "dir_no_listing",\n "path": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing",\n "dirname": "/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job ls] initial work dir {}\nINFO cwltool:job.py:266 [job ls] /private/tmp/docker_tmpe4wl6xjm$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpe4wl6xjm,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpy12k7j25,target=/tmp \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_deep_listing,target=/var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing,readonly \\\n --mount=type=bind,source=/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/dir_no_listing,target=/var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp3nblt4dz/20230605095055-445473.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n ls \\\n /var/lib/cwl/stgae1a4ad7-54fb-49d2-ad90-e7c0f6793d5f/dir_deep_listing \\\n /var/lib/cwl/stg7ab9a473-73ab-4448-b25c-5cc809ff34b1/dir_no_listing > /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 8cc5feedb2b21504d21859e0f63631f0b517553b metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 9b0f753abd9f52fa7bda09156130e6b0b936f1cd0705a6894db0eadff26b12a1 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: d6d5e13b344294994185ebcff17d42825d055b22a1e88978298377197522f2542db43987450874f4fd8da234a974070ce23ac03eff61c0a5a647d4c97a68cec6 metadata/directory-c91c2154-00bc-4457-bfda-4e377b7adce6.ttl\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/4a/4a0a19218e082a343a1b17e5333409af9d98f0f5\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/3c/3c363836cf4e16666669a25da280a1865c2d2874\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/58/58e6b3a414a1e090dfc6029add0f3555ccba127f\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 18386d0fde6d11e92ff3eb4475f6553b3093c775 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 31c7501fcee1311e24b50b4142dc0321239dbdaaf821e84c7370321898b234d3 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: be3cf5fc2ba70daafbc4cfe1fe3dd41ee9772f0cccd8f955aa6b0c619abb9eda2bc00818090ad245ffe663fb8151f5b965feb7f4933e3ce68e7d38ff89aa3587 metadata/directory-4bd4e38f-c825-4aa8-a7bb-cd7de8be06af.ttl\n\nINFO cwltool:job.py:905 [job ls] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/manifest-sha1.txt: a0ce0441f957dcde10291470aa5062ffc7cbdf8c data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\n\nDEBUG cwltool:ro.py:512 [provenance] Directory :dir_deep_listing\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nINFO cwltool:job.py:419 [job ls] completed success\nDEBUG cwltool:job.py:422 [job ls] outputs {\n "listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step ls] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/directory_no_listing.cwl#ls/listing": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n }\n}\nINFO cwltool:workflow_job.py:572 [step ls] completed success\nINFO cwltool:workflow_job.py:539 [workflow _17] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _17] outputs {\n "output_1": {\n "location": "file:///private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "basename": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameroot": "511f5ede99eeae60df68dedf0f5a3c2886774dad",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c",\n "size": 153,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e"\n },\n "output_2": {\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1",\n "basename": "dir1",\n "nameroot": "dir1",\n "nameext": "",\n "class": "Directory",\n "@id": "urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b",\n "listing": [\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a",\n "basename": "a",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b.txt",\n "basename": "b.txt",\n "checksum": "sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98",\n "@id": "urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059"\n },\n {\n "class": "Directory",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b",\n "basename": "b",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a/b/c.txt",\n "basename": "c.txt",\n "checksum": "sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4",\n "@id": "urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839"\n }\n ],\n "@id": "urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8"\n }\n ],\n "@id": "urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b"\n },\n {\n "class": "File",\n "location": "file:///private/tmp/docker_tmp30294ykg/dir1/a.txt",\n "basename": "a.txt",\n "checksum": "sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8",\n "@id": "urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d"\n }\n ]\n }\n}\nDEBUG cwltool:job.py:446 [job ls] Removing input staging directory /private/tmp/docker_tmphgdo2k_m\nDEBUG cwltool:job.py:454 [job ls] Removing temporary directory /private/tmp/docker_tmpy12k7j25\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpe4wl6xjm/511f5ede99eeae60df68dedf0f5a3c2886774dad to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp30294ykg/dir1 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpe4wl6xjm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp30294ykg\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp03q_qnzm\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 831d591ea563d82200f6b29cdbed89958af99946 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8591aab1f32872e19f186118be1462101272c003e5725780ad0a1053b4f45b8 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 1b73e532287cafb4438cfc69dd62ca998d374d25d2d2a9e1aae2d80da74193ec8abc5494227ed037b4a9cbcebd72b4ba2f5c5a995fc9406ad87abc08a421237a metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 52917a96deb1331e4f3e0d0c0ca5c06da11b550f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 952621e5f975fa4b8536d1246e03019673efe29716be7dd946885b26420ad858 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 9d13a8b2e9919c7d90a5b65c0af7326c4869efebe2b1525d1dee1d573159349fa8c3d9a06386e6e3054b4517ac86f5389bb90d9cc8105857baa9a142a9958123 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 4660384a529ef8217263414cfe7d8e09a36dae6a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: e8d43e02f50436e6bc3d92fdf3f37d0452a90fb55cc177c4902b62802ce733b8 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: c3a8205627d56adebcf5e2221b0ce6adc18bebc2af049dbec6dd744c90d1d704cca928860c5b41a8c0fa7056484ca8a454555ab058b982a5a5b3c4b48e35de1d metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: de4b6608f9e3af201c70ff6b53f85749a8492405 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: fadae5349308a66d763eacbe40b6c0348bdfd6947a138a8f8adab6c451836db5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 4eb4037e059930960700522093a233245189d1e1284b785d7642142d07ace00ecb89da2a98af756469be68dec3c3b6b0e41368ad4b0325b536fffb642fdc0280 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 153127a4ee5a028d1acd636b0809d434d53da02d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 717a4f8ae33902dcd217991e923892a59b626fe60f616d3cd275806d18e9da4a metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 5c8ece230a9c9d65f0b953c27045f92d27e3d6ecc3823e7ef9d3cb4426d66ded6a1fddd45a4bfed846940ed9a1f4bc3f4e9159650a856e9c7bdde1a7162f4ead metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 9a047fa31e52f7b66c1a7cebf88c57d9e388c8c6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: a727a73f4d563af8f90316d9ec809d0f853abc53632d2f306ca2944475293cdc metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 83f351fed5f621fa4763e6d0f0762964aa213f325926bf7c406e94eef34970695b9c599bfbd807565b497858edbdfbacc1c3001cbdfb54bb826e49da09ee004f metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'output_1\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}, \'output_2\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'basename\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameroot\': \'511f5ede99eeae60df68dedf0f5a3c2886774dad\', \'nameext\': \'\', \'class\': \'File\', \'checksum\': \'sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\', \'size\': 153, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/a0/a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 511f5ede99eeae60df68dedf0f5a3c2886774dad\nDEBUG cwltool:ro.py:591 [provenance] Relativising: \nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$a0ce0441f957dcde10291470aa5062ffc7cbdf8c\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 153\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:4933810d-08a1-4b8a-8ef5-d9172888367e\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1\', \'basename\': \'dir1\', \'nameroot\': \'dir1\', \'nameext\': \'\', \'class\': \'Directory\', \'@id\': \'urn:uuid:31d13089-c645-4929-aefa-b2363e5de52b\', \'listing\': [{\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': 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\'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}], \'@id\': \'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}, {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a\', \'basename\': \'a\', \'listing\': [{\'class\': \'File\', \'location\': 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\'urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}, {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b.txt\', \'basename\': \'b.txt\', \'checksum\': \'sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\', \'@id\': \'urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/e9/e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:ed6dc361-44fd-49f9-840a-fd761ca6c059\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'Directory\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b\', \'basename\': \'b\', \'listing\': [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}], \'@id\': \'urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Directory\nDEBUG cwltool:ro.py:591 [provenance] Relativising: b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a/b/c.txt\', \'basename\': \'c.txt\', \'checksum\': \'sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\', \'@id\': \'urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/84/84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: c.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$84a516841ba77a5b4648de2cd0dfcb30ea46dbb4\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:fed15753-4cd9-45ae-9825-8ac0addc9839\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f13fc0e-d432-4de8-8f20-b39d51151dd8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:a21c2d56-a76b-45d8-9a92-88ce71030a7b\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/cwltool-run/dir1/a.txt\', \'basename\': \'a.txt\', \'checksum\': \'sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\', \'@id\': \'urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/86/86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: a.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$86f7e437faa5a7fce15d1ddcb9eaeaea377667b8\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:b0de0cf4-2a48-4a5d-9903-e34807cb529d\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: a259a2ddea0fb8dbe04ce95431c7b87d74444c8d workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: f92dbdf72304f179e312894c469c59f4b08ddabf26264f1ad7a38aa6a527b39e workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 586e6634367c1f8cddf3f26d6e2c7ff826ce3677902c23890028d73f66b854b30eb013b70cecaefb3fdcb8f47fe266e7182f62f24b6f5d94973d73b7dbc04479 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 757937dc88f5d446a6e63c9d1f12acde32b02ecd snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 2c725914f45b19c49b5a6e9540477b70a0273cefdbd82c19de19054de16cb24f snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6d058c8a26fad02c7935f0ee249b186701f49d64ed43f8dccc87ca2f374356b971470006906e36f6d9c888cf50ead1e3fe3f6759e8d1d53a678ca6c1a171387a snapshot/directory_no_listing.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: ec85041b357ff2b39338cfbc69d2560640966f89 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 36a504d2c4551667e228d84c4eed90bd73747fe98606b30d912ec9b1ec3767bd metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: f2e20d11de50af96dc8e3bfcd43f0bc8d78342dda00c88c80de92a8f04d4aa3bbf684bf7c59f342cb8ef84393e00327a65b1c107d18f4a449e6116496d5e1f54 metadata/logs/engine.16cadf25-072f-4274-9fc5-0f3f605d8262.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0033518ae68cb74ef1d56196451d0ac9957ce80f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 640cf34ac826eeba52a190d69e5d9f3e0cd8025e6c6a20a5c32c5a479c687c67 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 6345ca41b6e0eedc5d3dc2a171ce96cb26aef6a6072f27634478eee2492ac756794ece6fd4949d827a922b55d0d2d7fd5c66b69ade15549c3b96aef4b86e9d0a metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha1.txt: 0d2331dab4d408bceb1057cfe5f1e826e1990c29 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha256.txt: 37908e47bb9f9ca212410631fd36ca1f333b9640b281b15639bfc1a822730ba6 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq/tagmanifest-sha512.txt: 059ed78b311c6402fb86010caf6283f0bd799fc922264bbef8b82bfb774e14680d16ee89810d4a50f82511d03a2a7596afe8806d3137f4c749d9db1e3b533ca2 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/4wm7h3qq\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_directory_workflow_no_lis0/provenance')], 'duration': 0.00152142999922944, 'start': 1685951456.977313, 'stop': 1685951456.978837, '$report_type': 'TestReport', 'item_index': 570, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_directory_workflow_no_listing - location: ('tests/test_provenance.py', 810, 'test_directory_workflow_no_listing') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - when: runtest - nodeid: tests/test_provenance.py::test_directory_workflow_no_listing - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print - location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print', 'location': ('tests/test_rdfprint.py', 10, 'test_rdf_print'), 'keywords': {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003581160008252482, 'start': 1685951456.985954, 'stop': 1685951456.986314, '$report_type': 'TestReport', 'item_index': 571, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_no_data_files', 'location': ('tests/test_provenance.py', 211, 'test_no_data_files'), 'keywords': {'test_no_data_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "required": null\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\'\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\n Source is from\n conditional step\n and may produce\n `null`\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\x1b[0m\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp3p2yoqwz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 76ff7ea1786cf066f9d27f62ce39dc7b8912ff90 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c25c8f928c17d87bf3d643440b193a6526d7ee708caa0c2e46a13d43ebca819f workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 5e670e3ab5fb07cfaf7271c5fd52eb799218d8c263bef6cf5d051ef829c3d5b9ab68c18099ac4c46e1fcc0d29481435a8d1e43f94f1ef389cb2ad25cda86d41c workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nWARNING cwltool:checker.py:319 Workflow checker warning:\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\n Source is from\n conditional step\n and may produce\n `null`\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp3p2yoqwz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {}\nDEBUG cwltool:workflow_job.py:678 [step step1_2] conditional $(self !== null) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step step1_2] inputs was {}\nINFO cwltool:workflow_job.py:744 [step step1_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl#step1/result": null\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {\n "required": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpw85wlbca\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 906879aff073b7271585c8e94b5e786399885ae4 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: a67c7989f08de0b1da9aeab47d3c36cebff617c52e186f7880b52e8589ab0763 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: a6f7ce24e8505d6efaac0991e836abcd8c94ff36b6abc4dd914e5d796e3f848af8e4e45d6fa81d0a292e94c73f30ac9f54cced88dfc7660f3ef20ded961bfd28 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: ef574f04f1f259da4bf821d7a723c4e0b4a16850 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 1aac2b40e29d4704822cf88b89b1a1c81786eb2cdcabfdce8f726584e6a18bac metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: c8fa7ad2a82c832407d2dd830992849721f80759ed32866acc0da5814d61359cf7703a8940a560135068080041eb79eb1284b72b9770ae74e115c926feca9b90 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 5de5a6348852a3f511f4d9b4c19534f843b6949e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 8006f09a7a98c509e354581b676fba851314f3baba8328121fc14fa45937500a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 8e0c7b84d0e4a2e4c1ba883c096d8f28bb358886da2e3e45ff9c7f5eaf60c355cc76bae84bbd07dbbb75f4b675aed8aa88b30ceac0db8af56a81f0f7922b1a97 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: a140d34e45e5963a13fd71358ca866c3d1ae4cfc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c4908a1f885bc4c25a7d1de051db8bb76f7d56cd69ea9d276f6792f6859c21ea metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: e4b03028f42b32b42dd65392b1c89a151ca3dd8d3fdcbaf2a106ddfbd50262d14766ad7ca26fba1d63204f69341ca37f069e148ba8ed04d315e5f0130d9ae303 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: dc447a9373f0695bc582d521621a7f82f4375e71 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c1c43ea92ba15d18b774ee73ffb5efb90e5d4facc26fa73c1b99322905b7d0e8 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: fd9082e819df9611218d883ec13873384a4082cb78d9ba0398d709857a339f2614638d1d428c3ca25c1448ab7b2932b8211f524806636a068befe6473106678b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 3605a04375d7d8d9c81476f2a090fb97cfe82e9e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 31f5626568b9723d0c92ada4c8fecfc29bd0a2cbc02b3a6725a777c8150a36a5 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 1a1d30fb8c9f171c9dfa355e7b42b58d7ff18131c3d3c88988c94002fe70e135f9900c76252cbc5f7fe83bf82829767d078f82071d1dec0bc81aa4a7a0529578 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'required\': None}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: None\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: c6eed93f6f7352dbaf7506c11290ad894b8a0ccc workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 9f3c0380c63d0919594109ffa5689d01ca1e706325627dd1e3f50cf3ccee5537 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: aec8768d19887675932326c35cce2c47d9c8013ab9750434c0f58116e0961efd5d167c421516d18272927ee3872b8cb5b6b4958be528f1cef32c05d51448af9e workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 0080e1d383e12bce874f3ab02b5127e32e49831d snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: f3ecdf078c82fa2b4bd0fcd6c2b8a667fa89defa4b2aa33522458f3877bed805 snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 51b39263588bfca976f0f429659ee9d4249b58f7d81f155a4beb26db5c43d254ffef1174e476666c1d6aa0ec8fc97502fbdc98a24914fc6de5a03c805e5d92bd snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 4306e1682fb3ca36fe69745e655e097c5a8bcd13 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: e92664a105c48f941c9a739505834a3368e5ed6dfd3d1fcbb8d6c40a44da1302 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 6bf26e1d8970422a37e70bb42087eb3df4fadc01f1eac160803014b4294b3b452f1621b4b3a31b3e3e558459024b81091cfdd6cb2eb8c004f38483d0daa18158 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: bce2e1c1aa51e5deabb2d0b32d996772cb0f1960 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 036230af7c59d21808d44fad73d73695b006dcf3195dfd2b0fe26ec3de4d97fc metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 16093a5882ed040e71b229d19014a842d0054e196baefaa8988764bd762db153b19b8606e9cb684c3edca2f0112f2248b7e7530b28c81641fb47b026aefed49c metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 2834064b00c5bb3e2b00dbdbbca5a3106d4b9704 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: f0db42848c92c60010a464280cc2186e58a408c8ecab72421fc7f3b3e09d02cf bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 5b261a0a305476a62385f00004676da3ae873889a94728d0b0b15e992658f4b9b3bb0c50b7895a72b9fe98cbf0ab4616f6c5d2b63f57321ccdec87f8c354b233 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance')], 'duration': 1.032393392000813, 'start': 1685951456.4351192, 'stop': 1685951457.467488, '$report_type': 'TestReport', 'item_index': 532, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_no_data_files', 'location': ('tests/test_provenance.py', 211, 'test_no_data_files'), 'keywords': {'test_no_data_files': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "required": null\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\'\n\x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\n Source is from\n conditional step\n and may produce\n `null`\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\x1b[0m\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp3p2yoqwz/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] will be skipped\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed skipped\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 76ff7ea1786cf066f9d27f62ce39dc7b8912ff90 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c25c8f928c17d87bf3d643440b193a6526d7ee708caa0c2e46a13d43ebca819f workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 5e670e3ab5fb07cfaf7271c5fd52eb799218d8c263bef6cf5d051ef829c3d5b9ab68c18099ac4c46e1fcc0d29481435a8d1e43f94f1ef389cb2ad25cda86d41c workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nWARNING cwltool:checker.py:319 Workflow checker warning:\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\n Source is from\n conditional step\n and may produce\n `null`\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:23:12: Source \'result\' of\n type ["null",\n "string"] may be\n incompatible\n../../../../../../../../../../../Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl:27:5: with sink\n \'required\' of type\n "string"\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp3p2yoqwz/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_2\nDEBUG cwltool:workflow_job.py:727 [step step1_2] job input {}\nDEBUG cwltool:workflow_job.py:678 [step step1_2] conditional $(self !== null) evaluated to False\nDEBUG cwltool:workflow_job.py:684 [step step1_2] inputs was {}\nINFO cwltool:workflow_job.py:744 [step step1_2] will be skipped\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conditional_step_no_inputs.cwl#step1/result": null\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed skipped\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {\n "required": null\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpw85wlbca\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 906879aff073b7271585c8e94b5e786399885ae4 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: a67c7989f08de0b1da9aeab47d3c36cebff617c52e186f7880b52e8589ab0763 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: a6f7ce24e8505d6efaac0991e836abcd8c94ff36b6abc4dd914e5d796e3f848af8e4e45d6fa81d0a292e94c73f30ac9f54cced88dfc7660f3ef20ded961bfd28 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: ef574f04f1f259da4bf821d7a723c4e0b4a16850 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 1aac2b40e29d4704822cf88b89b1a1c81786eb2cdcabfdce8f726584e6a18bac metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: c8fa7ad2a82c832407d2dd830992849721f80759ed32866acc0da5814d61359cf7703a8940a560135068080041eb79eb1284b72b9770ae74e115c926feca9b90 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 5de5a6348852a3f511f4d9b4c19534f843b6949e metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 8006f09a7a98c509e354581b676fba851314f3baba8328121fc14fa45937500a metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 8e0c7b84d0e4a2e4c1ba883c096d8f28bb358886da2e3e45ff9c7f5eaf60c355cc76bae84bbd07dbbb75f4b675aed8aa88b30ceac0db8af56a81f0f7922b1a97 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: a140d34e45e5963a13fd71358ca866c3d1ae4cfc metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c4908a1f885bc4c25a7d1de051db8bb76f7d56cd69ea9d276f6792f6859c21ea metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: e4b03028f42b32b42dd65392b1c89a151ca3dd8d3fdcbaf2a106ddfbd50262d14766ad7ca26fba1d63204f69341ca37f069e148ba8ed04d315e5f0130d9ae303 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: dc447a9373f0695bc582d521621a7f82f4375e71 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: c1c43ea92ba15d18b774ee73ffb5efb90e5d4facc26fa73c1b99322905b7d0e8 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: fd9082e819df9611218d883ec13873384a4082cb78d9ba0398d709857a339f2614638d1d428c3ca25c1448ab7b2932b8211f524806636a068befe6473106678b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 3605a04375d7d8d9c81476f2a090fb97cfe82e9e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 31f5626568b9723d0c92ada4c8fecfc29bd0a2cbc02b3a6725a777c8150a36a5 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 1a1d30fb8c9f171c9dfa355e7b42b58d7ff18131c3d3c88988c94002fe70e135f9900c76252cbc5f7fe83bf82829767d078f82071d1dec0bc81aa4a7a0529578 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'required\': None}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: None\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: c6eed93f6f7352dbaf7506c11290ad894b8a0ccc workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 9f3c0380c63d0919594109ffa5689d01ca1e706325627dd1e3f50cf3ccee5537 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: aec8768d19887675932326c35cce2c47d9c8013ab9750434c0f58116e0961efd5d167c421516d18272927ee3872b8cb5b6b4958be528f1cef32c05d51448af9e workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 0080e1d383e12bce874f3ab02b5127e32e49831d snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: f3ecdf078c82fa2b4bd0fcd6c2b8a667fa89defa4b2aa33522458f3877bed805 snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 51b39263588bfca976f0f429659ee9d4249b58f7d81f155a4beb26db5c43d254ffef1174e476666c1d6aa0ec8fc97502fbdc98a24914fc6de5a03c805e5d92bd snapshot/conditional_step_no_inputs.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 4306e1682fb3ca36fe69745e655e097c5a8bcd13 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: e92664a105c48f941c9a739505834a3368e5ed6dfd3d1fcbb8d6c40a44da1302 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 6bf26e1d8970422a37e70bb42087eb3df4fadc01f1eac160803014b4294b3b452f1621b4b3a31b3e3e558459024b81091cfdd6cb2eb8c004f38483d0daa18158 metadata/logs/engine.e22b9104-56a9-49ee-9854-e7b399df044d.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: bce2e1c1aa51e5deabb2d0b32d996772cb0f1960 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: 036230af7c59d21808d44fad73d73695b006dcf3195dfd2b0fe26ec3de4d97fc metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 16093a5882ed040e71b229d19014a842d0054e196baefaa8988764bd762db153b19b8606e9cb684c3edca2f0112f2248b7e7530b28c81641fb47b026aefed49c metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha1.txt: 2834064b00c5bb3e2b00dbdbbca5a3106d4b9704 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha256.txt: f0db42848c92c60010a464280cc2186e58a408c8ecab72421fc7f3b3e09d02cf bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0/tagmanifest-sha512.txt: 5b261a0a305476a62385f00004676da3ae873889a94728d0b0b15e992658f4b9b3bb0c50b7895a72b9fe98cbf0ab4616f6c5d2b63f57321ccdec87f8c354b233 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/j35b9hv0\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_no_data_files0/provenance')], 'duration': 0.0005033320003349218, 'start': 1685951457.468983, 'stop': 1685951457.4694881, '$report_type': 'TestReport', 'item_index': 532, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_no_data_files - location: ('tests/test_provenance.py', 211, 'test_no_data_files') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - when: runtest - nodeid: tests/test_provenance.py::test_no_data_files - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_absolute_path_fails - location: ('tests/test_provenance.py', 616, 'test_absolute_path_fails') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_absolute_path_fails', 'location': ('tests/test_provenance.py', 616, 'test_absolute_path_fails'), 'keywords': {'test_absolute_path_fails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5')], 'duration': 0.004511739999543352, 'start': 1685951457.471474, 'stop': 1685951457.475987, '$report_type': 'TestReport', 'item_index': 533, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_absolute_path_fails', 'location': ('tests/test_provenance.py', 616, 'test_absolute_path_fails'), 'keywords': {'test_absolute_path_fails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_absolute_path_fails0/tmpjwwvwmq5')], 'duration': 0.0004983560002074228, 'start': 1685951457.476467, 'stop': 1685951457.4769669, '$report_type': 'TestReport', 'item_index': 533, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_absolute_path_fails', 'location': ('tests/test_provenance.py', 616, 'test_absolute_path_fails'), 'keywords': {'test_absolute_path_fails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m 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{'nodeid': 'tests/test_provenance.py::test_climboutfails', 'location': ('tests/test_provenance.py', 621, 'test_climboutfails'), 'keywords': {'test_climboutfails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a')], 'duration': 0.004381741000543116, 'start': 1685951457.4802969, 'stop': 1685951457.48468, '$report_type': 'TestReport', 'item_index': 534, 'worker_id': 'gw6', 'testrun_uid': 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'tests/test_provenance.py::test_climboutfails', 'location': ('tests/test_provenance.py', 621, 'test_climboutfails'), 'keywords': {'test_climboutfails': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_climboutfails0/tmpa1ud_39a'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary 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('tests/test_provenance.py', 621, 'test_climboutfails') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_writable_string - location: ('tests/test_provenance.py', 626, 'test_writable_string') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_writable_string', 'location': ('tests/test_provenance.py', 626, 'test_writable_string'), 'keywords': {'test_writable_string': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: 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66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h/tagmanifest-sha512.txt: c2bad2223811194582af4d1508ac02cd69eeeeedeeb98d54fcae4dcefb13cc882e7640328206603d3fb9cd5f949a9be0db054dd34fbfa190c498a5fe09750cef file.txt')], 'duration': 0.0022833869998066803, 'start': 1685951457.4939451, 'stop': 1685951457.49623, '$report_type': 'TestReport', 'item_index': 535, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_writable_string', 'location': ('tests/test_provenance.py', 626, 'test_writable_string'), 'keywords': {'test_writable_string': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr setup', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h\x1b[0m\n'), ('Captured log setup', 'DEBUG cwltool:ro.py:95 [provenance] Temporary research object: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_string0/tmpreusg80h'), ('Captured stderr call', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Creating 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[provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha1.txt: f0abde070be90018bea62e64abc4a62757061888 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha256.txt: bb16a101c183c6c35bd53683d04273e214e77926e039369f065b11df84b47c80 file.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_writable_unicode_string0/tmpffpnl25d/tagmanifest-sha512.txt: e03ebad752a05a76268c9516807e8564af9a26827485e1e3525b06e1d784437a5e9455f764a9914f1a7b851ebfeab27127a5174955711b7e4fd2bfaa8057bd1b file.txt'), ('Captured stderr teardown', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[provenance] Deleting temporary 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location: ('tests/test_provenance.py', 658, 'test_writable_unicode_string') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_secrets.py::test_secret_workflow_log_override - location: ('tests/test_secrets.py', 101, 'test_secret_workflow_log_override') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log_override', 'location': ('tests/test_secrets.py', 101, 'test_secret_workflow_log_override'), 'keywords': {'test_secret_workflow_log_override': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00023334999968938064, 'start': 1685951457.511599, 'stop': 1685951457.5118332, '$report_type': 'TestReport', 'item_index': 585, 'worker_id': 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'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "path": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "dirname": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj3ojtpk2$ cat \\\n /private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/امتحان > /private/tmp/docker_tmpj3ojtpk2/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj3ojtpk2/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmpe7iqwjai\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmpq5u7xb8a\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj3ojtpk2/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj3ojtpk2\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "path": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "dirname": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj3ojtpk2$ cat \\\n /private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/امتحان > /private/tmp/docker_tmpj3ojtpk2/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj3ojtpk2/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmpe7iqwjai\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmpq5u7xb8a\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj3ojtpk2/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj3ojtpk2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.718482084000243, 'start': 1685951456.926538, 'stop': 1685951457.645005, '$report_type': 'TestReport', 'item_index': 502, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]'), 'keywords': {'test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": ""\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "path": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "dirname": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] /private/tmp/docker_tmpj3ojtpk2$ cat \\\n /private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/امتحان > /private/tmp/docker_tmpj3ojtpk2/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj3ojtpk2/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing input staging directory /private/tmp/docker_tmpe7iqwjai\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_6] Removing temporary directory /private/tmp/docker_tmpq5u7xb8a\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpj3ojtpk2/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpj3ojtpk2\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_6] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/script\nDEBUG cwltool:command_line_tool.py:988 [job script_6] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": ""\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_6] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "size": 0,\n "basename": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameroot": "\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "nameext": "",\n "path": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646",\n "dirname": "/private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_6] initial work dir {}\nINFO cwltool:job.py:266 [job script_6] /private/tmp/docker_tmpj3ojtpk2$ cat \\\n /private/tmp/docker_tmpe7iqwjai/stg2172807a-db04-4b29-88a3-e20578171d8b/امتحان > /private/tmp/docker_tmpj3ojtpk2/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_6] completed success\nDEBUG cwltool:job.py:422 [job script_6] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpj3ojtpk2/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_6] Removing input staging directory /private/tmp/docker_tmpe7iqwjai\nDEBUG cwltool:job.py:454 [job script_6] Removing temporary directory /private/tmp/docker_tmpq5u7xb8a\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpj3ojtpk2/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files__u5/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpj3ojtpk2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008691729999554809, 'start': 1685951457.6467788, 'stop': 1685951457.647649, '$report_type': 'TestReport', 'item_index': 502, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_input_files[\u0627\u0645\u062a\u062d\u0627\u0646] - location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[\\u0627\\u0645\\u062a\\u062d\\u0627\\u0646]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_input_files[abc+DEFGZ.z_12345-] - location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[abc+DEFGZ.z_12345-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_input_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016044889998738654, 'start': 1685951457.65006, 'stop': 1685951457.651665, '$report_type': 'TestReport', 'item_index': 503, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print', 'location': ('tests/test_rdfprint.py', 10, 'test_rdf_print'), 'keywords': {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '@prefix CommandLineBinding: .\n@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n cwl:inputBinding [ CommandLineBinding:position 1 ] ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'")], 'duration': 0.6995283690002907, 'start': 1685951456.986822, 'stop': 1685951457.686334, '$report_type': 'TestReport', 'item_index': 571, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print', 'location': ('tests/test_rdfprint.py', 10, 'test_rdf_print'), 'keywords': {'test_rdf_print': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '@prefix CommandLineBinding: .\n@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n cwl:inputBinding [ CommandLineBinding:position 1 ] ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'")], 'duration': 0.00019048600006499328, 'start': 1685951457.686794, 'stop': 1685951457.686985, '$report_type': 'TestReport', 'item_index': 571, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print - location: ('tests/test_rdfprint.py', 10, 'test_rdf_print') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print_unicode - location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print_unicode', 'location': ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode'), 'keywords': {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005043370001658332, 'start': 1685951457.688944, 'stop': 1685951457.68945, '$report_type': 'TestReport', 'item_index': 572, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log', 'location': ('tests/test_secrets.py', 59, 'test_secret_workflow_log'), 'keywords': {'test_secret_workflow_log': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "path": "/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19"\n }\n}'), ('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl",\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_job.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "example.conf"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job step1] initial work dir {\n "_:a013850b-7da3-40b4-b8b0-9956d7c5d457": [\n "username: user\\npassword: (secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)\\n",\n "/YZQNYw/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp1kf06cap$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp1kf06cap,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp0hnprorq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpxnlrl83i/20230605095056-771506.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/debian:stable-slim \\\n cat \\\n example.conf > /private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpjged9yh3\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmp0hnprorq\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1kf06cap\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp36ys10ak\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 3.3611989219998577, 'start': 1685951454.434431, 'stop': 1685951457.795549, '$report_type': 'TestReport', 'item_index': 583, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log', 'location': ('tests/test_secrets.py', 59, 'test_secret_workflow_log'), 'keywords': {'test_secret_workflow_log': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "path": "/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19"\n }\n}'), ('Captured stderr call', 'stable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl",\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _14] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _14] start\nDEBUG cwltool:workflow_job.py:777 [workflow _14] inputs {\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nINFO cwltool:workflow_job.py:613 [workflow _14] starting step step1\nDEBUG cwltool:workflow_job.py:727 [step step1] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nINFO cwltool:workflow_job.py:75 [step step1] start\nDEBUG cwltool:command_line_tool.py:982 [job step1] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_job.cwl as part of step step1\nDEBUG cwltool:command_line_tool.py:988 [job step1] {\n "pw": "(secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "example.conf"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job step1] initial work dir {\n "_:a013850b-7da3-40b4-b8b0-9956d7c5d457": [\n "username: user\\npassword: (secret-c4a00e42-efc9-4d0e-aefa-e0a481772a55)\\n",\n "/YZQNYw/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1] /private/tmp/docker_tmp1kf06cap$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp1kf06cap,target=/YZQNYw \\\n --mount=type=bind,source=/private/tmp/docker_tmp0hnprorq,target=/tmp \\\n --workdir=/YZQNYw \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpxnlrl83i/20230605095056-771506.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/YZQNYw \\\n docker.io/debian:stable-slim \\\n cat \\\n example.conf > /private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19\nINFO cwltool:job.py:905 [job step1] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1] completed success\nDEBUG cwltool:job.py:422 [job step1] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1] completed success\nINFO cwltool:workflow_job.py:539 [workflow _14] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _14] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1] Removing input staging directory /private/tmp/docker_tmpjged9yh3\nDEBUG cwltool:job.py:454 [job step1] Removing temporary directory /private/tmp/docker_tmp0hnprorq\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1kf06cap/bc8b5192097de6a54afeeb064f187d67a8cfff19 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp7j97v4s3/bc8b5192097de6a54afeeb064f187d67a8cfff19\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1kf06cap\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp36ys10ak\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00046288000066851964, 'start': 1685951457.797031, 'stop': 1685951457.7974951, '$report_type': 'TestReport', 'item_index': 583, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_secrets.py::test_secret_workflow_log - location: ('tests/test_secrets.py', 59, 'test_secret_workflow_log') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_secrets.py::test_secret_workflow_log_singularity - location: ('tests/test_secrets.py', 80, 'test_secret_workflow_log_singularity') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log_singularity', 'location': ('tests/test_secrets.py', 80, 'test_secret_workflow_log_singularity'), 'keywords': {'test_secret_workflow_log_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_secrets.py', 81, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003086459992118762, 'start': 1685951457.800096, 'stop': 1685951457.800406, '$report_type': 'TestReport', 'item_index': 584, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log_singularity', 'location': ('tests/test_secrets.py', 80, 'test_secret_workflow_log_singularity'), 'keywords': {'test_secret_workflow_log_singularity': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003312149992780178, 'start': 1685951457.801483, 'stop': 1685951457.801816, '$report_type': 'TestReport', 'item_index': 584, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_secrets.py::test_secret_workflow_log_singularity - location: ('tests/test_secrets.py', 80, 'test_secret_workflow_log_singularity') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_singularity.py::test_singularity2_docker_image_id_in_tool - location: ('tests/test_singularity.py', 114, 'test_singularity2_docker_image_id_in_tool') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity.py::test_singularity2_docker_image_id_in_tool', 'location': ('tests/test_singularity.py', 114, 'test_singularity2_docker_image_id_in_tool'), 'keywords': {'test_singularity2_docker_image_id_in_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 115, 'Skipped: Requires that version 2.6.x of singularity executable version is on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00026410500049678376, 'start': 1685951457.802933, 'stop': 1685951457.803199, '$report_type': 'TestReport', 'item_index': 591, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity.py::test_singularity2_docker_image_id_in_tool', 'location': ('tests/test_singularity.py', 114, 'test_singularity2_docker_image_id_in_tool'), 'keywords': {'test_singularity2_docker_image_id_in_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0001863429997683852, 'start': 1685951457.803916, 'stop': 1685951457.8041039, '$report_type': 'TestReport', 'item_index': 591, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_singularity.py::test_singularity2_docker_image_id_in_tool - location: ('tests/test_singularity.py', 114, 'test_singularity2_docker_image_id_in_tool') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_singularity.py::test_singularity3_docker_image_id_in_tool - location: ('tests/test_singularity.py', 138, 'test_singularity3_docker_image_id_in_tool') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity.py::test_singularity3_docker_image_id_in_tool', 'location': ('tests/test_singularity.py', 138, 'test_singularity3_docker_image_id_in_tool'), 'keywords': {'test_singularity3_docker_image_id_in_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 139, 'Skipped: Requires that version 3.x of singularity executable version is on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002477910002198769, 'start': 1685951457.804945, 'stop': 1685951457.805194, '$report_type': 'TestReport', 'item_index': 592, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity.py::test_singularity3_docker_image_id_in_tool', 'location': ('tests/test_singularity.py', 138, 'test_singularity3_docker_image_id_in_tool'), 'keywords': {'test_singularity3_docker_image_id_in_tool': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0003100769999946351, 'start': 1685951457.805884, 'stop': 1685951457.806195, '$report_type': 'TestReport', 'item_index': 592, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_singularity.py::test_singularity3_docker_image_id_in_tool - location: ('tests/test_singularity.py', 138, 'test_singularity3_docker_image_id_in_tool') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_singularity_versions.py::test_get_version - location: ('tests/test_singularity_versions.py', 32, 'test_get_version') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity_versions.py::test_get_version', 'location': ('tests/test_singularity_versions.py', 32, 'test_get_version'), 'keywords': {'test_get_version': 1, 'test_singularity_versions.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002954239998871344, 'start': 1685951457.808606, 'stop': 1685951457.808903, '$report_type': 'TestReport', 'item_index': 593, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity_versions.py::test_get_version', 'location': ('tests/test_singularity_versions.py', 32, 'test_get_version'), 'keywords': {'test_get_version': 1, 'test_singularity_versions.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:57]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32mSingularity version: 1.0.1 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pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_input_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": 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"test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "path": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "dirname": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_7] /private/tmp/docker_tmpb7jiejr4$ cat \\\n /private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345- > /private/tmp/docker_tmpb7jiejr4/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpb7jiejr4/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] Removing input staging directory /private/tmp/docker_tmpbm414g78\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] Removing temporary directory /private/tmp/docker_tmp4f26hj3w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpb7jiejr4/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpb7jiejr4\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_7] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_7] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_7] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "path": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "dirname": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_7] initial work dir {}\nINFO cwltool:job.py:266 [job script_7] /private/tmp/docker_tmpb7jiejr4$ cat \\\n /private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345- > /private/tmp/docker_tmpb7jiejr4/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_7] completed success\nDEBUG cwltool:job.py:422 [job script_7] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpb7jiejr4/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_7] Removing input staging directory /private/tmp/docker_tmpbm414g78\nDEBUG cwltool:job.py:454 [job script_7] Removing temporary directory /private/tmp/docker_tmp4f26hj3w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpb7jiejr4/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpb7jiejr4\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.654889022000134, 'start': 1685951457.652152, 'stop': 1685951458.3070269, '$report_type': 'TestReport', 'item_index': 503, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_input_files[abc+DEFGZ.z_12345-]', 'location': ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[abc+DEFGZ.z_12345-]'), 'keywords': {'test_unicode_in_input_files[abc+DEFGZ.z_12345-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'abc+DEFGZ.z_12345-': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-"\n },\n "output": "test.txt"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "path": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "dirname": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_7] /private/tmp/docker_tmpb7jiejr4$ cat \\\n /private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345- > /private/tmp/docker_tmpb7jiejr4/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpb7jiejr4/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] Removing input staging directory /private/tmp/docker_tmpbm414g78\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_7] Removing temporary directory /private/tmp/docker_tmp4f26hj3w\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpb7jiejr4/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpb7jiejr4\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_7] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_7] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-"\n },\n "output": "test.txt"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_7] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/abc+DEFGZ.z_12345-",\n "size": 0,\n "basename": "abc+DEFGZ.z_12345-",\n "nameroot": "abc+DEFGZ",\n "nameext": ".z_12345-",\n "path": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345-",\n "dirname": "/private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_7] initial work dir {}\nINFO cwltool:job.py:266 [job script_7] /private/tmp/docker_tmpb7jiejr4$ cat \\\n /private/tmp/docker_tmpbm414g78/stg71747e25-9849-4888-a571-bf5a7e62c23c/abc+DEFGZ.z_12345- > /private/tmp/docker_tmpb7jiejr4/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_7] completed success\nDEBUG cwltool:job.py:422 [job script_7] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpb7jiejr4/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_7] Removing input staging directory /private/tmp/docker_tmpbm414g78\nDEBUG cwltool:job.py:454 [job script_7] Removing temporary directory /private/tmp/docker_tmp4f26hj3w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpb7jiejr4/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_input_files_ab0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpb7jiejr4\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007895850003478699, 'start': 1685951458.308804, 'stop': 1685951458.3095949, '$report_type': 'TestReport', 'item_index': 503, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_input_files[abc+DEFGZ.z_12345-] - location: ('tests/test_path_checks.py', 61, 'test_unicode_in_input_files[abc+DEFGZ.z_12345-]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u6e2c\u8a66] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u6e2c\\u8a66]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u6e2c\\u8a66]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u6e2c\\u8a66]'), 'keywords': {'test_unicode_in_output_files[\\u6e2c\\u8a66]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u6e2c\\u8a66': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001846268000008422, 'start': 1685951458.312243, 'stop': 1685951458.31409, '$report_type': 'TestReport', 'item_index': 504, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_output', 'location': ('tests/test_stdout_stderr_log_dir.py', 6, 'test_log_dir_echo_output'), 'keywords': {'test_log_dir_echo_output': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl] {\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n "inp"\n ],\n "datum": "hello"\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl] /private/tmp/docker_tmpwfwddvpw$ echo \\\n hello > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_log_dir_echo_output0/echo.cwl/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl] outputs {\n "out": "hello\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl] Removing input staging directory /private/tmp/docker_tmp55k4p0um\nDEBUG cwltool:job.py:454 [job echo.cwl] Removing temporary directory /private/tmp/docker_tmpaxet3r4x\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwfwddvpw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7238111329997992, 'start': 1685951457.819371, 'stop': 1685951458.5431669, '$report_type': 'TestReport', 'item_index': 595, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_output', 'location': ('tests/test_stdout_stderr_log_dir.py', 6, 'test_log_dir_echo_output'), 'keywords': {'test_log_dir_echo_output': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo.cwl] {\n "inp": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n "inp"\n ],\n "datum": "hello"\n }\n]\nDEBUG cwltool:job.py:215 [job echo.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job echo.cwl] /private/tmp/docker_tmpwfwddvpw$ echo \\\n hello > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_log_dir_echo_output0/echo.cwl/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo.cwl] completed success\nDEBUG cwltool:job.py:422 [job echo.cwl] outputs {\n "out": "hello\\n"\n}\nDEBUG cwltool:job.py:446 [job echo.cwl] Removing input staging directory /private/tmp/docker_tmp55k4p0um\nDEBUG cwltool:job.py:454 [job echo.cwl] Removing temporary directory /private/tmp/docker_tmpaxet3r4x\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpwfwddvpw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000621432999651006, 'start': 1685951458.544076, 'stop': 1685951458.544699, '$report_type': 'TestReport', 'item_index': 595, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_output - location: ('tests/test_stdout_stderr_log_dir.py', 6, 'test_log_dir_echo_output') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_no_output - location: ('tests/test_stdout_stderr_log_dir.py', 22, 'test_log_dir_echo_no_output') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_no_output', 'location': ('tests/test_stdout_stderr_log_dir.py', 22, 'test_log_dir_echo_no_output'), 'keywords': {'test_log_dir_echo_no_output': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001245518999894557, 'start': 1685951458.546586, 'stop': 1685951458.5478332, '$report_type': 'TestReport', 'item_index': 596, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow', 'location': ('tests/test_provenance.py', 74, 'test_revsort_workflow'), 'keywords': {'test_revsort_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "sorted_output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt",\n "basename": "output.txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step rev\n\x1b[1;30mINFO\x1b[0m [step rev] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\n\x1b[1;30mINFO\x1b[0m [job rev] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job rev] completed success\n\x1b[1;30mINFO\x1b[0m [step rev] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step sorted\n\x1b[1;30mINFO\x1b[0m [step sorted] start\n\x1b[1;30mINFO\x1b[0m [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\n\x1b[1;30mINFO\x1b[0m [job sorted] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job sorted] completed success\n\x1b[1;30mINFO\x1b[0m [step sorted] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\', job_order=[\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}, \'reverse_sort\': True}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b9792322151224743947536605dc9cca24e185d8 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 0b54605194d27895bfbccb163d89b64dba40161d9771e915b204ef89c0501446 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 924e606ff3341e4daea625839633159c1a0c71d12d64532f78160aa03284c5537f3726613c5fa3ec938e0cb3972113e20f4fde6617c88cc98f7e6ec6001e31b5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n },\n "reverse_sort": true\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step rev\nDEBUG cwltool:workflow_job.py:727 [step rev] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step rev] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step rev] start\nDEBUG cwltool:command_line_tool.py:982 [job rev] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/revtool.cwl as part of step rev\nDEBUG cwltool:command_line_tool.py:988 [job rev] {\n "revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job rev] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job rev] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "revtool_input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "dirname": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job rev] initial work dir {}\nINFO cwltool:job.py:266 [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:job.py:905 [job rev] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 97fe1b50b4582cebc7d853796ebd62e3e163aa3f data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nINFO cwltool:job.py:419 [job rev] completed success\nDEBUG cwltool:job.py:422 [job rev] outputs {\n "revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step rev] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:572 [step rev] completed success\nDEBUG cwltool:job.py:446 [job rev] Removing input staging directory /private/tmp/docker_tmp0onaxo3l\nDEBUG cwltool:job.py:454 [job rev] Removing temporary directory /private/tmp/docker_tmpwl097n7z\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step sorted\nDEBUG cwltool:workflow_job.py:727 [step sorted] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step sorted] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:75 [step sorted] start\nDEBUG cwltool:command_line_tool.py:982 [job sorted] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sorttool.cwl as part of step sorted\nDEBUG cwltool:command_line_tool.py:988 [job sorted] {\n "reverse": true,\n "sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job sorted] path mappings is {\n "file:///private/tmp/docker_tmpo8j3qsh0/output.txt": [\n "/private/tmp/docker_tmpo8j3qsh0/output.txt",\n "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job sorted] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sort"\n },\n {\n "position": [\n 1,\n "reverse"\n ],\n "prefix": "--reverse",\n "datum": true\n },\n {\n "position": [\n 2,\n "sorted_input"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1",\n "path": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "dirname": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job sorted] initial work dir {}\nINFO cwltool:job.py:266 [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\nINFO cwltool:job.py:905 [job sorted] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: b9214658cc453331b62c2282b772a5c063dbd284 data/b9/b9214658cc453331b62c2282b772a5c063dbd284\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nINFO cwltool:job.py:419 [job sorted] completed success\nDEBUG cwltool:job.py:422 [job sorted] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step sorted] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step sorted] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:job.py:446 [job sorted] Removing input staging directory /private/tmp/docker_tmpt9i2u3d_\nDEBUG cwltool:job.py:454 [job sorted] Removing temporary directory /private/tmp/docker_tmp7ypgmrbr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplkmwaaf_/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplkmwaaf_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp46e4pq4y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo8j3qsh0\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: df915edbd6b5e75857277eb6c8e1377f0d051ef1 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4e56225fad8da955eebc34f2c094def00b9a7b6b39c500bd4ba036618c22e6f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 42a067ea2914371f209f8c25161dee0d1589e739c64f3275519f23d0af480afc636ea8b3298663632e89b2033c18a855ad9eb5290298ed00837688a946ac1523 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 553157706bf95e14c524a396a623d0f3f87f8ecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c6eccb1bc96bd4f55d03be6f4c0262a736dd8296ecae60d0d403bc9bfc8ca92b metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: f8c2586c8f0749fe5ef9e772f752c63acc2ba9dc8176e2cd8da9e677b952f7ba5a8410f062937ee19a3db25b2a414ef3566294dec7e6b6d011f21d176f3e4e3f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: ca44d2cee82bdf4159a998516a8b7d97de4becde metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 9abbc3a964398906a0a6c446f05be412b4f818c5df80213eefb95585644407f9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4dd04bc545f060056ec3c0eb38c22e70e30c30f4b3d633c60a802e4fcb4607737e7938f57b1eaea5a7044b23bf39461a15ccd68a344564b0a257cb7c966d8562 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b52bb0536caa8678dee76e093bab66c9f6ab72d8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fe046d6822ede74b785f00faa9e38aeeb92d573926c5e8f0dc3e87ddcf655336 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 3fe06b96dca53c5afed7eee93e58b27dd8330c34ce5436271af797259e4ffbc9790bb32f8cdab7244e1a83d0f8f1137464dc0dd757d841ac69412932cf09a9f9 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e58bcf95cb06e3d42132d9c488c389eb62de0170 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 27f34aff0b66f02249b46599489c42e37efc5de28e05274bba403a11a31bd86e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4f70440a6e4c80363471248e4d36d4df1a61f6bdeebdc41391bab98dcc5715361142776d4dd4dcc2b9f81d4687b83ea3a259c4a52374d0e6bed988bb6cfc8683 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: bb4d8f1c88da465df4d205fe71778cf5ee0c971e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 45e8790efb18825deb4c136d97032976f831b167076b31e43bd6ae66fc7466d7 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: bad9c61094a072702da2befe78c06dc406039eba8d4f5abeb39fb0646589428829d6e32ce91b705be4d0b9eba94cad5ca02e0665a23e9190438ef61b05611244 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'sorted_output\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 0536da382206c737b78578fb4cd56d470854cb65 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: ca8f0addfb91188dc24d6f6f2455b58ba794fa05417a99e239993ca8a25627c4 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 1ecd7b38f4685c4c7c7a124deaf30613ef849999f7aa5afb3b537d294a9e66933052c4e35fcb2d7a37e565e33a918c497349b9fc901cf828c5f9cd592dce1114 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: eac590a030efa84e4abe5c70bfbbe059d59cb909 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c85344af5e84a113da5636b4c42935c478fe1b587b2f84f82aa07465a71ce1d1 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fc05d8795084ee56e93edfd135c625c462e71dfaed99a7dc613264eb2b8a75a518580a187fb580fa9309c4cb1398a6501040c6251a221f31cbe67c5576a5d799 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: a7199d53b1f707ab9bfa7a88f832a843a05da1b5 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 44dad89d06c949f171fb43e2c2a870f92520a7d288460cafadfd19afefb7697c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fed9bf631358efdec9cb96154215b41a76dc6b7cd38eeb794f6a94212e5fcf868dcc776b0cec9d950de8370d3e4399a7c36833da2d5bdebfb0e193d813047ad4 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 825bbdb1ae0c5b4dab6115409f478fd2b7546ef1 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 65c5c5444143e944a90a7ec7fed5e89f3b4195f53a84f0747bca4875ad8602ec bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 9212abe820053e53692266203ba3819ceae75bb7f5d82f74281d7d1e9e0682ee506d9b210ef2d2bae5396e8d0f751bafbdf1f361747bf3cdc4d9aaa247919f25 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance')], 'duration': 4.937757239000348, 'start': 1685951453.6408331, 'stop': 1685951458.578468, '$report_type': 'TestReport', 'item_index': 525, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow', 'location': ('tests/test_provenance.py', 74, 'test_revsort_workflow'), 'keywords': {'test_revsort_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "sorted_output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt",\n "basename": "output.txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mINFO\x1b[0m [workflow _16] start\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step rev\n\x1b[1;30mINFO\x1b[0m [step rev] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/debian:stable-slim']\nstable-slim: Pulling from library/debian\nDigest: sha256:d828cca5497a2519da9c6d42372066895fa28a69f1e8a46a38ce8f750bd2adf0\nStatus: Image is up to date for debian:stable-slim\ndocker.io/library/debian:stable-slim\n\x1b[1;30mINFO\x1b[0m [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\n\x1b[1;30mINFO\x1b[0m [job rev] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job rev] completed success\n\x1b[1;30mINFO\x1b[0m [step rev] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] starting step sorted\n\x1b[1;30mINFO\x1b[0m [step sorted] start\n\x1b[1;30mINFO\x1b[0m [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\n\x1b[1;30mINFO\x1b[0m [job sorted] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job sorted] completed success\n\x1b[1;30mINFO\x1b[0m [step sorted] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _16] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\', job_order=[\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpfvs6cctm/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}, \'reverse_sort\': True}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b9792322151224743947536605dc9cca24e185d8 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 0b54605194d27895bfbccb163d89b64dba40161d9771e915b204ef89c0501446 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 924e606ff3341e4daea625839633159c1a0c71d12d64532f78160aa03284c5537f3726613c5fa3ec938e0cb3972113e20f4fde6617c88cc98f7e6ec6001e31b5 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _16] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:workflow_job.py:765 [workflow _16] start\nDEBUG cwltool:workflow_job.py:777 [workflow _16] inputs {\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n },\n "reverse_sort": true\n}\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step rev\nDEBUG cwltool:workflow_job.py:727 [step rev] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step rev] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step rev] start\nDEBUG cwltool:command_line_tool.py:982 [job rev] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/revtool.cwl as part of step rev\nDEBUG cwltool:command_line_tool.py:988 [job rev] {\n "revtool_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job rev] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job rev] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "rev"\n },\n {\n "position": [\n 0,\n "revtool_input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt",\n "path": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt",\n "dirname": "/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/debian:stable-slim\']\nDEBUG cwltool:job.py:215 [job rev] initial work dir {}\nINFO cwltool:job.py:266 [job rev] /private/tmp/docker_tmpo8j3qsh0$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpwl097n7z,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpzvli50o1/20230605095056-122780.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n rev \\\n /var/lib/cwl/stgbfeb172c-18a8-44e7-b778-e279f1c6cdec/whale.txt > /private/tmp/docker_tmpo8j3qsh0/output.txt\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nINFO cwltool:job.py:905 [job rev] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: 97fe1b50b4582cebc7d853796ebd62e3e163aa3f data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/97/97fe1b50b4582cebc7d853796ebd62e3e163aa3f\nINFO cwltool:job.py:419 [job rev] completed success\nDEBUG cwltool:job.py:422 [job rev] outputs {\n "revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step rev] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#rev/revtool_output": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:572 [step rev] completed success\nDEBUG cwltool:job.py:446 [job rev] Removing input staging directory /private/tmp/docker_tmp0onaxo3l\nDEBUG cwltool:job.py:454 [job rev] Removing temporary directory /private/tmp/docker_tmpwl097n7z\nINFO cwltool:workflow_job.py:613 [workflow _16] starting step sorted\nDEBUG cwltool:workflow_job.py:727 [step sorted] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step sorted] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/reverse": true,\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nINFO cwltool:workflow_job.py:75 [step sorted] start\nDEBUG cwltool:command_line_tool.py:982 [job sorted] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sorttool.cwl as part of step sorted\nDEBUG cwltool:command_line_tool.py:988 [job sorted] {\n "reverse": true,\n "sorted_input": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job sorted] path mappings is {\n "file:///private/tmp/docker_tmpo8j3qsh0/output.txt": [\n "/private/tmp/docker_tmpo8j3qsh0/output.txt",\n "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job sorted] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "sort"\n },\n {\n "position": [\n 1,\n "reverse"\n ],\n "prefix": "--reverse",\n "datum": true\n },\n {\n "position": [\n 2,\n "sorted_input"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpo8j3qsh0/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:1437d081-ca8d-4a80-8b11-06f127985ff1",\n "path": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt",\n "dirname": "/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job sorted] initial work dir {}\nINFO cwltool:job.py:266 [job sorted] /private/tmp/docker_tmplkmwaaf_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmplkmwaaf_,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmp7ypgmrbr,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpo8j3qsh0/output.txt,target=/var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp94ufptbh/20230605095057-173607.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/debian:stable-slim \\\n sort \\\n --reverse \\\n /var/lib/cwl/stg25efb018-d8e3-483c-b449-c35188745f49/output.txt > /private/tmp/docker_tmplkmwaaf_/output.txt\nINFO cwltool:job.py:905 [job sorted] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/manifest-sha1.txt: b9214658cc453331b62c2282b772a5c063dbd284 data/b9/b9214658cc453331b62c2282b772a5c063dbd284\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nINFO cwltool:job.py:419 [job sorted] completed success\nDEBUG cwltool:job.py:422 [job sorted] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step sorted] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl#sorted/sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step sorted] completed success\nINFO cwltool:workflow_job.py:539 [workflow _16] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _16] outputs {\n "sorted_output": {\n "location": "file:///private/tmp/docker_tmplkmwaaf_/output.txt",\n "basename": "output.txt",\n "nameroot": "output",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",\n "size": 1111,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5"\n }\n}\nDEBUG cwltool:job.py:446 [job sorted] Removing input staging directory /private/tmp/docker_tmpt9i2u3d_\nDEBUG cwltool:job.py:454 [job sorted] Removing temporary directory /private/tmp/docker_tmp7ypgmrbr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmplkmwaaf_/output.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplkmwaaf_\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp46e4pq4y\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpo8j3qsh0\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: df915edbd6b5e75857277eb6c8e1377f0d051ef1 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4e56225fad8da955eebc34f2c094def00b9a7b6b39c500bd4ba036618c22e6f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 42a067ea2914371f209f8c25161dee0d1589e739c64f3275519f23d0af480afc636ea8b3298663632e89b2033c18a855ad9eb5290298ed00837688a946ac1523 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 553157706bf95e14c524a396a623d0f3f87f8ecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c6eccb1bc96bd4f55d03be6f4c0262a736dd8296ecae60d0d403bc9bfc8ca92b metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: f8c2586c8f0749fe5ef9e772f752c63acc2ba9dc8176e2cd8da9e677b952f7ba5a8410f062937ee19a3db25b2a414ef3566294dec7e6b6d011f21d176f3e4e3f metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: ca44d2cee82bdf4159a998516a8b7d97de4becde metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 9abbc3a964398906a0a6c446f05be412b4f818c5df80213eefb95585644407f9 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4dd04bc545f060056ec3c0eb38c22e70e30c30f4b3d633c60a802e4fcb4607737e7938f57b1eaea5a7044b23bf39461a15ccd68a344564b0a257cb7c966d8562 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: b52bb0536caa8678dee76e093bab66c9f6ab72d8 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fe046d6822ede74b785f00faa9e38aeeb92d573926c5e8f0dc3e87ddcf655336 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 3fe06b96dca53c5afed7eee93e58b27dd8330c34ce5436271af797259e4ffbc9790bb32f8cdab7244e1a83d0f8f1137464dc0dd757d841ac69412932cf09a9f9 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e58bcf95cb06e3d42132d9c488c389eb62de0170 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 27f34aff0b66f02249b46599489c42e37efc5de28e05274bba403a11a31bd86e metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4f70440a6e4c80363471248e4d36d4df1a61f6bdeebdc41391bab98dcc5715361142776d4dd4dcc2b9f81d4687b83ea3a259c4a52374d0e6bed988bb6cfc8683 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: bb4d8f1c88da465df4d205fe71778cf5ee0c971e metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 45e8790efb18825deb4c136d97032976f831b167076b31e43bd6ae66fc7466d7 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: bad9c61094a072702da2befe78c06dc406039eba8d4f5abeb39fb0646589428829d6e32ce91b705be4d0b9eba94cad5ca02e0665a23e9190438ef61b05611244 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'sorted_output\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/cwltool-run/output.txt\', \'basename\': \'output.txt\', \'nameroot\': \'output\', \'nameext\': \'.txt\', \'class\': \'File\', \'checksum\': \'sha1$b9214658cc453331b62c2282b772a5c063dbd284\', \'size\': 1111, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/b9/b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: output\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$b9214658cc453331b62c2282b772a5c063dbd284\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:0f0dd99e-3a69-4345-8e60-e441ebdd64d5\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 0536da382206c737b78578fb4cd56d470854cb65 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: ca8f0addfb91188dc24d6f6f2455b58ba794fa05417a99e239993ca8a25627c4 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 1ecd7b38f4685c4c7c7a124deaf30613ef849999f7aa5afb3b537d294a9e66933052c4e35fcb2d7a37e565e33a918c497349b9fc901cf828c5f9cd592dce1114 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: eac590a030efa84e4abe5c70bfbbe059d59cb909 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: c85344af5e84a113da5636b4c42935c478fe1b587b2f84f82aa07465a71ce1d1 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fc05d8795084ee56e93edfd135c625c462e71dfaed99a7dc613264eb2b8a75a518580a187fb580fa9309c4cb1398a6501040c6251a221f31cbe67c5576a5d799 metadata/logs/engine.e454983d-73e2-4441-aaa8-548bbd4af896.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: a7199d53b1f707ab9bfa7a88f832a843a05da1b5 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 44dad89d06c949f171fb43e2c2a870f92520a7d288460cafadfd19afefb7697c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: fed9bf631358efdec9cb96154215b41a76dc6b7cd38eeb794f6a94212e5fcf868dcc776b0cec9d950de8370d3e4399a7c36833da2d5bdebfb0e193d813047ad4 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha1.txt: 825bbdb1ae0c5b4dab6115409f478fd2b7546ef1 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha256.txt: 65c5c5444143e944a90a7ec7fed5e89f3b4195f53a84f0747bca4875ad8602ec bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v/tagmanifest-sha512.txt: 9212abe820053e53692266203ba3819ceae75bb7f5d82f74281d7d1e9e0682ee506d9b210ef2d2bae5396e8d0f751bafbdf1f361747bf3cdc4d9aaa247919f25 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/evmwbv7v\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow0/provenance')], 'duration': 0.0007942510001157643, 'start': 1685951458.580619, 'stop': 1685951458.581415, '$report_type': 'TestReport', 'item_index': 525, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_revsort_workflow - location: ('tests/test_provenance.py', 74, 'test_revsort_workflow') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - when: runtest - nodeid: tests/test_provenance.py::test_revsort_workflow - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut - location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow_shortcut', 'location': ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut'), 'keywords': {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014417179991141893, 'start': 1685951458.583897, 'stop': 1685951458.5853388, '$report_type': 'TestReport', 'item_index': 526, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u6e2c\\u8a66]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u6e2c\\u8a66]'), 'keywords': {'test_unicode_in_output_files[\\u6e2c\\u8a66]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u6e2c\\u8a66': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/%E6%B8%AC%E8%A9%A6",\n "basename": "測試",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test"\n },\n "output": "\\u6e2c\\u8a66"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u6e2c\\u8a66"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "dirname": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_8] /private/tmp/docker_tmpvb00lkdp$ cat \\\n /private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test > /private/tmp/docker_tmpvb00lkdp/測試\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_8] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvb00lkdp/%E6%B8%AC%E8%A9%A6",\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] Removing input staging directory /private/tmp/docker_tmpj0hp0cs6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] Removing temporary directory /private/tmp/docker_tmpm9tfik8b\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpvb00lkdp/測試 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvb00lkdp\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test"\n },\n "output": "\\u6e2c\\u8a66"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_8] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_8] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u6e2c\\u8a66"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_8] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "dirname": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_8] initial work dir {}\nINFO cwltool:job.py:266 [job script_8] /private/tmp/docker_tmpvb00lkdp$ cat \\\n /private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test > /private/tmp/docker_tmpvb00lkdp/測試\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_8] completed success\nDEBUG cwltool:job.py:422 [job script_8] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvb00lkdp/%E6%B8%AC%E8%A9%A6",\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_8] Removing input staging directory /private/tmp/docker_tmpj0hp0cs6\nDEBUG cwltool:job.py:454 [job script_8] Removing temporary directory /private/tmp/docker_tmpm9tfik8b\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvb00lkdp/測試 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvb00lkdp\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.739881903999958, 'start': 1685951458.314523, 'stop': 1685951459.054388, '$report_type': 'TestReport', 'item_index': 504, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_path_checks.py::test_unicode_in_output_files[\\u6e2c\\u8a66]', 'location': ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u6e2c\\u8a66]'), 'keywords': {'test_unicode_in_output_files[\\u6e2c\\u8a66]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, '\\u6e2c\\u8a66': 1, 'test_path_checks.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/%E6%B8%AC%E8%A9%A6",\n "basename": "測試",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\'\n../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script#output\' previously defined\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test"\n },\n "output": "\\u6e2c\\u8a66"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u6e2c\\u8a66"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "dirname": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_8] /private/tmp/docker_tmpvb00lkdp$ cat \\\n /private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test > /private/tmp/docker_tmpvb00lkdp/測試\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_8] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvb00lkdp/%E6%B8%AC%E8%A9%A6",\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] Removing input staging directory /private/tmp/docker_tmpj0hp0cs6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_8] Removing temporary directory /private/tmp/docker_tmpm9tfik8b\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpvb00lkdp/測試 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpvb00lkdp\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\'\nWARNING salad:ref_resolver.py:1130 ../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script:10:5: object id \'../../../../private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script#output\' previously defined\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test"\n },\n "output": "\\u6e2c\\u8a66"\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_8] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_8] {\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": ""\n },\n "output": "\\u6e2c\\u8a66"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_8] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/test",\n "size": 0,\n "basename": "test",\n "nameroot": "test",\n "nameext": "",\n "path": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test",\n "dirname": "/private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_8] initial work dir {}\nINFO cwltool:job.py:266 [job script_8] /private/tmp/docker_tmpvb00lkdp$ cat \\\n /private/tmp/docker_tmpj0hp0cs6/stg74fbe865-b43b-4701-8c02-fa3edbe55cc7/test > /private/tmp/docker_tmpvb00lkdp/測試\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_8] completed success\nDEBUG cwltool:job.py:422 [job script_8] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpvb00lkdp/%E6%B8%AC%E8%A9%A6",\n "basename": "\\u6e2c\\u8a66",\n "nameroot": "\\u6e2c\\u8a66",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_8] Removing input staging directory /private/tmp/docker_tmpj0hp0cs6\nDEBUG cwltool:job.py:454 [job script_8] Removing temporary directory /private/tmp/docker_tmpm9tfik8b\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvb00lkdp/測試 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_unicode_in_output_files__0/outdir/測試\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvb00lkdp\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007373680000455352, 'start': 1685951459.0556428, 'stop': 1685951459.056383, '$report_type': 'TestReport', 'item_index': 504, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_path_checks.py::test_unicode_in_output_files[\u6e2c\u8a66] - location: ('tests/test_path_checks.py', 85, 'test_unicode_in_output_files[\\u6e2c\\u8a66]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_stderr - location: ('tests/test_stdout_stderr_log_dir.py', 43, 'test_log_dir_echo_stderr') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_stderr', 'location': ('tests/test_stdout_stderr_log_dir.py', 43, 'test_log_dir_echo_stderr'), 'keywords': {'test_log_dir_echo_stderr': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018100770003002253, 'start': 1685951459.058351, 'stop': 1685951459.060163, '$report_type': 'TestReport', 'item_index': 597, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 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09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9odb_yg_/stgca46d439-209c-4d1e-bb58-97f4594c7017/tmp",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] command line bindings is []\x1b[0m\n'), ('Captured log call', 'DEBUG cwltool:command_line_tool.py:982 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] initializing from _:ff671d66-28a2-4132-960c-1afd90ca1e6a\nDEBUG cwltool:command_line_tool.py:988 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] {\n "inp": {\n "class": "File",\n "location": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "streamable": false,\n "basename": "tmp",\n "nameroot": "tmp",\n "nameext": "",\n "size": 0\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] path mappings is {\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_input_can_be_named_pipe_F1/tmp",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/9odb_yg_/stgca46d439-209c-4d1e-bb58-97f4594c7017/tmp",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ff671d66-28a2-4132-960c-1afd90ca1e6a_3] command line bindings is []')], 'duration': 0.0003800060003413819, 'start': 1685951459.293602, 'stop': 1685951459.293983, '$report_type': 'TestReport', 'item_index': 602, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[False-False-True] - location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[False-False-True]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] - location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0]', 'location': ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]'), 'keywords': {'test_subclass_CLT[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0006368040003508213, 'start': 1685951459.294997, 'stop': 1685951459.295636, '$report_type': 'TestReport', 'item_index': 603, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0]', 'location': ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]'), 'keywords': {'test_subclass_CLT[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.004742043999613088, 'start': 1685951459.296237, 'stop': 1685951459.300981, '$report_type': 'TestReport', 'item_index': 603, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log_override', 'location': ('tests/test_secrets.py', 101, 'test_secret_workflow_log_override'), 'keywords': {'test_secret_workflow_log_override': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmps8bqpoe9/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "path": "/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmps8bqpoe9/bc8b5192097de6a54afeeb064f187d67a8cfff19"\n }\n}'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl",\n "pw": "Hoopla!"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "pw": "Hoopla!"\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "Hoopla!"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "Hoopla!"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_job.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "pw": "Hoopla!"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {\n "_:efa2380f-a71c-428d-b7d9-1ac6fbb22b99": [\n "username: user\\npassword: Hoopla!\\n",\n "/ZYBRaV/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpdjx8sgdx$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdjx8sgdx,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1pq6g9g1,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2ewi2yx1/20230605095058-275748.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n cat \\\n example.conf > /private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19\nINFO cwltool:job.py:905 [job step1_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpor336_66\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmp1pq6g9g1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmps8bqpoe9/bc8b5192097de6a54afeeb064f187d67a8cfff19\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmxm82p8l\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdjx8sgdx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.7880733340007282, 'start': 1685951457.512193, 'stop': 1685951459.3002229, '$report_type': 'TestReport', 'item_index': 585, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0]', 'location': ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]'), 'keywords': {'test_subclass_CLT[snippet0]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet0': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002549229993746849, 'start': 1685951459.301441, 'stop': 1685951459.301697, '$report_type': 'TestReport', 'item_index': 603, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secret_workflow_log_override', 'location': ('tests/test_secrets.py', 101, 'test_secret_workflow_log_override'), 'keywords': {'test_secret_workflow_log_override': 1, 'skipif': 1, 'pytestmark': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": {\n "location": "file:///var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmps8bqpoe9/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "path": "/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmps8bqpoe9/bc8b5192097de6a54afeeb064f187d67a8cfff19"\n }\n}'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl",\n "pw": "Hoopla!"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "pw": "Hoopla!"\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "Hoopla!"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/pw": "Hoopla!"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_job.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "pw": "Hoopla!"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n 0,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {\n "_:efa2380f-a71c-428d-b7d9-1ac6fbb22b99": [\n "username: user\\npassword: Hoopla!\\n",\n "/ZYBRaV/example.conf",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpdjx8sgdx$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdjx8sgdx,target=/ZYBRaV \\\n --mount=type=bind,source=/private/tmp/docker_tmp1pq6g9g1,target=/tmp \\\n --workdir=/ZYBRaV \\\n --read-only=true \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2ewi2yx1/20230605095058-275748.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/ZYBRaV \\\n docker.io/debian:stable-slim \\\n cat \\\n example.conf > /private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19\nINFO cwltool:job.py:905 [job step1_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/secret_wf.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "basename": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameroot": "bc8b5192097de6a54afeeb064f187d67a8cfff19",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$e334a15593ba7b48b383db009f249d6524bfadf7",\n "size": 33,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpor336_66\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmp1pq6g9g1\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdjx8sgdx/bc8b5192097de6a54afeeb064f187d67a8cfff19 to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmps8bqpoe9/bc8b5192097de6a54afeeb064f187d67a8cfff19\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpmxm82p8l\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdjx8sgdx\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0004045150008096243, 'start': 1685951459.301536, 'stop': 1685951459.301941, '$report_type': 'TestReport', 'item_index': 585, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_CLT[snippet0] - location: ('tests/test_subclass_mypyc.py', 21, 'test_subclass_CLT[snippet0]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_secrets.py::test_secret_workflow_log_override - location: ('tests/test_secrets.py', 101, 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0.0003865159997076262, 'start': 1685951459.3204029, 'stop': 1685951459.32079, '$report_type': 'TestReport', 'item_index': 606, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1]', 'location': ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]'), 'keywords': {'test_subclass_exprtool[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.006563943999935873, 'start': 1685951459.321141, 'stop': 1685951459.327706, '$report_type': 'TestReport', 'item_index': 606, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1]', 'location': ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]'), 'keywords': {'test_subclass_exprtool[snippet1]': 1, 'parametrize': 1, 'pytestmark': 1, 'snippet1': 1, 'test_subclass_mypyc.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00027535600020200945, 'start': 1685951459.328183, 'stop': 1685951459.328459, '$report_type': 'TestReport', 'item_index': 606, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subclass_mypyc.py::test_subclass_exprtool[snippet1] - location: ('tests/test_subclass_mypyc.py', 32, 'test_subclass_exprtool[snippet1]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints - location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqshints', 'location': ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints'), 'keywords': {'test_single_process_inherit_reqshints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013924539998697583, 'start': 1685951459.329356, 'stop': 1685951459.330749, '$report_type': 'TestReport', 'item_index': 611, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_get_subgraph', 'location': ('tests/test_subgraph.py', 26, 'test_get_subgraph'), 'keywords': {'test_get_subgraph': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1\x1b[0m\n"), ('Captured log call', "WARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.14068840500021906, 'start': 1685951459.316004, 'stop': 1685951459.456691, '$report_type': 'TestReport', 'item_index': 608, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_get_subgraph', 'location': ('tests/test_subgraph.py', 26, 'test_get_subgraph'), 'keywords': {'test_get_subgraph': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1\x1b[0m\n"), ('Captured log call', "WARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.00024345899964828277, 'start': 1685951459.457286, 'stop': 1685951459.45753, '$report_type': 'TestReport', 'item_index': 608, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_get_subgraph - location: ('tests/test_subgraph.py', 26, 'test_get_subgraph') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_get_subgraph_long_out_form - location: ('tests/test_subgraph.py', 55, 'test_get_subgraph_long_out_form') - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_get_subgraph_long_out_form', 'location': ('tests/test_subgraph.py', 55, 'test_get_subgraph_long_out_form'), 'keywords': {'test_get_subgraph_long_out_form': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003143270005239174, 'start': 1685951459.4586198, 'stop': 1685951459.458936, '$report_type': 'TestReport', 'item_index': 609, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] -pif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'te pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_relocate.py::test_for_910', 'location': ('tests/test_relocate.py', 14, 'test_for_910'), 'keywords': {'test_for_910': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output_folder": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default",\n "basename": "default",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt",\n "basename": "file.txt",\n "checksum": "sha1$7b502c3a1f48c8609ae212cdfb639dee39673f5e",\n "size": 11,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default"\n }\n}{\n "output_folder": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default",\n "basename": "default",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt",\n "basename": "file.txt",\n "checksum": "sha1$7b502c3a1f48c8609ae212cdfb639dee39673f5e",\n "size": 11,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl'\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/ubuntu']\nUsing default tag: latest\nlatest: Pulling from library/ubuntu\nDigest: sha256:ac58ff7fe25edc58bdf0067ca99df00014dbd032e2246d30a722fa348fd799a5\nStatus: Image is up to date for ubuntu:latest\ndocker.io/library/ubuntu:latest\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] /private/tmp/docker_tmp_5jmo05k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_5jmo05k,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpampehdwa,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4rhkd8q4/20230605095056-803929.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\ndefault\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl'\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] /private/tmp/docker_tmpdqmzp90p$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqmzp90p,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp7x3ibbqw,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp9i7465r8/20230605095058-538883.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\ndefault\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job 910.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\nDEBUG cwltool:command_line_tool.py:988 [job 910.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job 910.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job 910.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/ubuntu\']\nDEBUG cwltool:job.py:215 [job 910.cwl] initial work dir {\n "_:3e29ab95-b40b-4874-b53d-3e3a756b4ffc": [\n "_:3e29ab95-b40b-4874-b53d-3e3a756b4ffc",\n "/GbFKKR/default",\n "WritableDirectory",\n true\n ],\n "_:3a6ea71c-e219-453f-ae43-5fcd8b01c76b": [\n "Hello world",\n "/GbFKKR/default/file.txt",\n "CreateWritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 910.cwl] /private/tmp/docker_tmp_5jmo05k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_5jmo05k,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpampehdwa,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4rhkd8q4/20230605095056-803929.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\nINFO cwltool:job.py:905 [job 910.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job 910.cwl] completed success\nDEBUG cwltool:job.py:422 [job 910.cwl] outputs {\n "output_folder": {\n "location": "file:///private/tmp/docker_tmp_5jmo05k/default",\n "basename": "default",\n "nameroot": "default",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job 910.cwl] Removing input staging directory /private/tmp/docker_tmp2fseafki\nDEBUG cwltool:job.py:454 [job 910.cwl] Removing temporary directory /private/tmp/docker_tmpampehdwa\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_5jmo05k/default to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_5jmo05k\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job 910.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\nDEBUG cwltool:command_line_tool.py:988 [job 910.cwl_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job 910.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job 910.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job 910.cwl_2] initial work dir {\n "_:9bd8d9fb-ba21-4479-86cb-92132d242768": [\n "_:9bd8d9fb-ba21-4479-86cb-92132d242768",\n "/GbFKKR/default",\n "WritableDirectory",\n true\n ],\n "_:461b72fd-438a-46ec-9b5f-b069b8590be0": [\n "Hello world",\n "/GbFKKR/default/file.txt",\n "CreateWritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 910.cwl_2] /private/tmp/docker_tmpdqmzp90p$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqmzp90p,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp7x3ibbqw,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp9i7465r8/20230605095058-538883.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\nINFO cwltool:job.py:905 [job 910.cwl_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job 910.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job 910.cwl_2] outputs {\n "output_folder": {\n "location": "file:///private/tmp/docker_tmpdqmzp90p/default",\n "basename": "default",\n "nameroot": "default",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job 910.cwl_2] Removing input staging directory /private/tmp/docker_tmpwt5tsqil\nDEBUG cwltool:job.py:454 [job 910.cwl_2] Removing temporary directory /private/tmp/docker_tmp7x3ibbqw\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdqmzp90p/default to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdqmzp90p/default/file.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdqmzp90p\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 4.948344170000382, 'start': 1685951454.617118, 'stop': 1685951459.5653398, '$report_type': 'TestReport', 'item_index': 574, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_relocate.py::test_for_910', 'location': ('tests/test_relocate.py', 14, 'test_for_910'), 'keywords': {'test_for_910': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output_folder": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default",\n "basename": "default",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt",\n "basename": "file.txt",\n "checksum": "sha1$7b502c3a1f48c8609ae212cdfb639dee39673f5e",\n "size": 11,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default"\n }\n}{\n "output_folder": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default",\n "basename": "default",\n "class": "Directory",\n "listing": [\n {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt",\n "basename": "file.txt",\n "checksum": "sha1$7b502c3a1f48c8609ae212cdfb639dee39673f5e",\n "size": 11,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt"\n }\n ],\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl'\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/ubuntu']\nUsing default tag: latest\nlatest: Pulling from library/ubuntu\nDigest: sha256:ac58ff7fe25edc58bdf0067ca99df00014dbd032e2246d30a722fa348fd799a5\nStatus: Image is up to date for ubuntu:latest\ndocker.io/library/ubuntu:latest\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] /private/tmp/docker_tmp_5jmo05k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_5jmo05k,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpampehdwa,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4rhkd8q4/20230605095056-803929.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\ndefault\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job 910.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl'\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] /private/tmp/docker_tmpdqmzp90p$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqmzp90p,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp7x3ibbqw,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp9i7465r8/20230605095058-538883.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\ndefault\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job 910.cwl_2] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job 910.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\nDEBUG cwltool:command_line_tool.py:988 [job 910.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job 910.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job 910.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/ubuntu\']\nDEBUG cwltool:job.py:215 [job 910.cwl] initial work dir {\n "_:3e29ab95-b40b-4874-b53d-3e3a756b4ffc": [\n "_:3e29ab95-b40b-4874-b53d-3e3a756b4ffc",\n "/GbFKKR/default",\n "WritableDirectory",\n true\n ],\n "_:3a6ea71c-e219-453f-ae43-5fcd8b01c76b": [\n "Hello world",\n "/GbFKKR/default/file.txt",\n "CreateWritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 910.cwl] /private/tmp/docker_tmp_5jmo05k$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_5jmo05k,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmpampehdwa,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp4rhkd8q4/20230605095056-803929.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\nINFO cwltool:job.py:905 [job 910.cwl] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job 910.cwl] completed success\nDEBUG cwltool:job.py:422 [job 910.cwl] outputs {\n "output_folder": {\n "location": "file:///private/tmp/docker_tmp_5jmo05k/default",\n "basename": "default",\n "nameroot": "default",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job 910.cwl] Removing input staging directory /private/tmp/docker_tmp2fseafki\nDEBUG cwltool:job.py:454 [job 910.cwl] Removing temporary directory /private/tmp/docker_tmpampehdwa\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_5jmo05k/default to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_5jmo05k\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/910.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job 910.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/910.cwl\nDEBUG cwltool:command_line_tool.py:988 [job 910.cwl_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job 910.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job 910.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "ls"\n }\n]\nDEBUG cwltool:job.py:215 [job 910.cwl_2] initial work dir {\n "_:9bd8d9fb-ba21-4479-86cb-92132d242768": [\n "_:9bd8d9fb-ba21-4479-86cb-92132d242768",\n "/GbFKKR/default",\n "WritableDirectory",\n true\n ],\n "_:461b72fd-438a-46ec-9b5f-b069b8590be0": [\n "Hello world",\n "/GbFKKR/default/file.txt",\n "CreateWritableFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job 910.cwl_2] /private/tmp/docker_tmpdqmzp90p$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpdqmzp90p,target=/GbFKKR \\\n --mount=type=bind,source=/private/tmp/docker_tmp7x3ibbqw,target=/tmp \\\n --workdir=/GbFKKR \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp9i7465r8/20230605095058-538883.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/GbFKKR \\\n docker.io/ubuntu \\\n ls\nINFO cwltool:job.py:905 [job 910.cwl_2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job 910.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job 910.cwl_2] outputs {\n "output_folder": {\n "location": "file:///private/tmp/docker_tmpdqmzp90p/default",\n "basename": "default",\n "nameroot": "default",\n "nameext": "",\n "class": "Directory"\n }\n}\nDEBUG cwltool:job.py:446 [job 910.cwl_2] Removing input staging directory /private/tmp/docker_tmpwt5tsqil\nDEBUG cwltool:job.py:454 [job 910.cwl_2] Removing temporary directory /private/tmp/docker_tmp7x3ibbqw\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdqmzp90p/default to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpdqmzp90p/default/file.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_9100/default/file.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpdqmzp90p\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008282369999506045, 'start': 1685951459.567082, 'stop': 1685951459.5679119, '$report_type': 'TestReport', 'item_index': 574, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_relocate.py::test_for_910 - location: ('tests/test_relocate.py', 14, 'test_for_910') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_relocate.py::test_for_conflict_file_names - location: ('tests/test_relocate.py', 20, 'test_for_conflict_file_names') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names', 'location': ('tests/test_relocate.py', 20, 'test_for_conflict_file_names'), 'keywords': {'test_for_conflict_file_names': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0013990580000609043, 'start': 1685951459.5697222, 'stop': 1685951459.571127, '$report_type': 'TestReport', 'item_index': 575, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print_unicode', 'location': ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode'), 'keywords': {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix rdfs: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n rdfs:label "Sequence file in FASTA format" ;\n rdfs:comment """Input sequence file in FASTA format (not compressed/zipped!).\nCan be an assembled genome (genome mode) or transcriptome (DNA,\ntranscriptome mode), or protein sequences from an annotated gene set\n(proteins mode).\nNB: select just one transcript/protein per gene for your input,\notherwise they will appear as ‘Duplicated’ matches.\n""" ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m /Users/jasperk/gitlab/cwltool/cwltool/__main__.py 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl'\n")], 'duration': 1.9449515790001897, 'start': 1685951457.6899168, 'stop': 1685951459.634825, '$report_type': 'TestReport', 'item_index': 572, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_rdfprint.py::test_rdf_print_unicode', 'location': ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode'), 'keywords': {'test_rdf_print_unicode': 1, 'test_rdfprint.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '@prefix cwl: .\n@prefix ns1: .\n@prefix rdf: .\n@prefix rdfs: .\n@prefix sld: .\n@prefix xsd: .\n\n a cwl:CommandLineTool ;\n ns1:original_cwlVersion "v1.0" ;\n cwl:baseCommand ( "echo" ) ;\n cwl:cwlVersion ;\n cwl:hints [ a ],\n [ a ] ;\n cwl:inputs .\n\n rdfs:label "Sequence file in FASTA format" ;\n rdfs:comment """Input sequence file in FASTA format (not compressed/zipped!).\nCan be an assembled genome (genome mode) or transcriptome (DNA,\ntranscriptome mode), or protein sequences from an annotated gene set\n(proteins mode).\nNB: select just one transcript/protein per gene for your input,\notherwise they will appear as ‘Duplicated’ matches.\n""" ;\n sld:type xsd:string .\n\n\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m /Users/jasperk/gitlab/cwltool/cwltool/__main__.py 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/utf_doc_example.cwl'\n")], 'duration': 0.0006568690005224198, 'start': 1685951459.6365361, 'stop': 1685951459.637194, '$report_type': 'TestReport', 'item_index': 572, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_rdfprint.py::test_rdf_print_unicode - location: ('tests/test_rdfprint.py', 14, 'test_rdf_print_unicode') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_singularity.py::test_singularity_iwdr - location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity.py::test_singularity_iwdr', 'location': ('tests/test_singularity.py', 62, 'test_singularity_iwdr'), 'keywords': {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.002171388000533625, 'start': 1685951459.638792, 'stop': 1685951459.6409652, '$report_type': 'TestReport', 'item_index': 588, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow_shortcut', 'location': ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut'), 'keywords': {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'failed', 'longrepr': {'reprcrash': {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 46, 'message': "AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))\nassert 1 == 0"}, 'reprtraceback': {'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_revsort_workflow_shortcut(tmp_path: Path) -> None:', ' """Confirm that using \'cwl:tool\' shortcut still snapshots the CWL files."""', '> folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/revsort-job-shortcut.json"),', ' )'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 89, 'message': ''}, 'style': 'long'}}, {'type': 'ReprEntry', 'data': {'lines': [' def cwltool(tmp_path: Path, *args: Any) -> Path:', ' prov_folder = tmp_path / "provenance"', ' prov_folder.mkdir()', ' new_args = ["--provenance", str(prov_folder)]', ' new_args.extend(args)', ' # Run within a temporary directory to not pollute git checkout', ' tmp_dir = tmp_path / "cwltool-run"', ' tmp_dir.mkdir()', ' with working_directory(tmp_dir):', ' status = main(new_args)', '> assert status == 0, f"Failed: cwltool.main({args})"', "E AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))", 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')"), ('args', "('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',)"), ('prov_folder', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')"), ('new_args', "['--provenance', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance', '/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json']"), ('tmp_dir', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 46, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, 'sections': [], 'chain': [({'reprentries': [{'type': 'ReprEntry', 'data': {'lines': [' @needs_docker', ' def test_revsort_workflow_shortcut(tmp_path: Path) -> None:', ' """Confirm that using \'cwl:tool\' shortcut still snapshots the CWL files."""', '> folder = cwltool(', ' tmp_path,', ' get_data("tests/wf/revsort-job-shortcut.json"),', ' )'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 89, 'message': ''}, 'style': 'long'}}, {'type': 'ReprEntry', 'data': {'lines': [' def cwltool(tmp_path: Path, *args: Any) -> Path:', ' prov_folder = tmp_path / "provenance"', ' prov_folder.mkdir()', ' new_args = ["--provenance", str(prov_folder)]', ' new_args.extend(args)', ' # Run within a temporary directory to not pollute git checkout', ' tmp_dir = tmp_path / "cwltool-run"', ' tmp_dir.mkdir()', ' with working_directory(tmp_dir):', ' status = main(new_args)', '> assert status == 0, f"Failed: cwltool.main({args})"', "E AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))", 'E assert 1 == 0'], 'reprfuncargs': {'args': [('tmp_path', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0')"), ('args', "('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',)"), ('prov_folder', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')"), ('new_args', "['--provenance', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance', '/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json']"), ('tmp_dir', "PosixPath('/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run')")]}, 'reprlocals': None, 'reprfileloc': {'path': 'tests/test_provenance.py', 'lineno': 46, 'message': 'AssertionError'}, 'style': 'long'}}], 'extraline': None, 'style': 'long'}, {'path': '/Users/jasperk/gitlab/cwltool/tests/test_provenance.py', 'lineno': 46, 'message': "AssertionError: Failed: cwltool.main(('/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json',))\nassert 1 == 0"}, None)]}, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mERROR\x1b[0m \x1b[31mGot workflow error\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json",\n "reverse_sort": true,\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "@id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'reverse_sort\': True, \'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 5e5a492f53d25bdd4e5e7e3ee61407036d74c263 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 8322e8a8c8231f681484b7cf2caae8110994310a49cbb0679a9dc40993bd863d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 57b1439b4885ea2220eb4b4177e0c82d5724d29dd75ce4ce5b4041c9a9c705cadc478ed732165222d7fff8788ef51dc4c5478ae1586d34fa3bec637b183cdcd6 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nERROR cwltool:executors.py:250 Got workflow error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: d4e780eac6b995170c5544138e51cee42bf82b02 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 71854d40af17ddaad25710ff92bed3033edc5312cea32640d1780241b99df51f metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: ba634748b2a242590fe4f2f293ea32ab4cae028fc7ba9a83b3ce2964374030766b9b71e13fe231a9e27877e79b5c939c949ce2cab6806a002f4ef8005ea34504 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: fa166224b2884b8c1a7019701241269f0fe8f4ba metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: b220ef2e9661453dc089f3645d905eb38ede5f81267288875ebaa393f440a3b6 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 67dc40c370f4eb425ad35887933493d90057b10fb0d6c65a7b9dd47fd482ce515036fe98304f7a6254891a4240f1f515e792dd7c3610f9d4e38c5954de185854 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 7b845a04531a0aea8b66445b3cb5dfd3cc38987e bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 674fc7391ca2a9c892cc4a7b8f6d69ef84f4debea78506708c389a4611090a94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 350e30ea50137627007116ea6a7b9e3f71a7b9e01835e5e0b82201f45bd7f577cc3f294c98401c2afabc72bd7c331d4a7ad8cb70dcac056749b3d897311a5e03 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')], 'duration': 0.9283330289999867, 'start': 1685951458.585697, 'stop': 1685951459.514008, '$report_type': 'TestReport', 'item_index': 526, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('failed', 'F', 'FAILED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_revsort_workflow_shortcut', 'location': ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut'), 'keywords': {'test_revsort_workflow_shortcut': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\n\x1b[1;30mERROR\x1b[0m \x1b[31mGot workflow error\x1b[0m\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 8bcf8ada87c0a350de5d54cdd483c63a56aac1df workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 063ced41ac308f393023a79870a8915541de4fedc2f2943391d77d11a0a0fa83 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 041f48a61e00f67357aa19bda91035b2e28afd0a391dccf8e05b8d71b7b8de8c34c55f3e175d99e55d14f8fbacc0902f903e269a7c786739a19f450ba63c66fa workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpat6bw7o5/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/revsort-job-shortcut.json",\n "reverse_sort": true,\n "workflow_input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "format": "https://www.iana.org/assignments/media-types/text/plain",\n "@id": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'reverse_sort\': True, \'workflow_input\': {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: True\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'format\': \'https://www.iana.org/assignments/media-types/text/plain\', \'@id\': \'file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\', \'size\': 1111, \'basename\': \'whale.txt\', \'nameroot\': \'whale\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/manifest-sha1.txt: 327fc7aedf4f6b69a42a7c8b808dc5a7aff61376 data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:591 [provenance] Relativising: https://www.iana.org/assignments/media-types/text/plain\nDEBUG cwltool:ro.py:591 [provenance] Relativising: file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 1111\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: whale\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 5e5a492f53d25bdd4e5e7e3ee61407036d74c263 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 8322e8a8c8231f681484b7cf2caae8110994310a49cbb0679a9dc40993bd863d workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 57b1439b4885ea2220eb4b4177e0c82d5724d29dd75ce4ce5b4041c9a9c705cadc478ed732165222d7fff8788ef51dc4c5478ae1586d34fa3bec637b183cdcd6 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _17] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/revsort.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/32/327fc7aedf4f6b69a42a7c8b808dc5a7aff61376\nERROR cwltool:executors.py:250 Got workflow error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/executors.py", line 231, in run_jobs\n prov_obj.evaluate(\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 247, in evaluate\n self.used_artefacts(customised_job, self.workflow_run_uri)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 623, in used_artefacts\n entity = self.declare_artefact(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 528, in declare_artefact\n (entity, _, _) = self.declare_file(value)\n File "/Users/jasperk/gitlab/cwltool/cwltool/cwlprov/provenance_profile.py", line 333, in declare_file\n file_entity = self.document.entity(\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1630, in entity\n return self.new_record(PROV_ENTITY, identifier, None, other_attributes)\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 1605, in new_record\n new_record = PROV_REC_CLS[record_type](\n File "/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/prov/model.py", line 552, in __init__\n raise ProvElementIdentifierRequired()\nprov.model.ProvElementIdentifierRequired: An identifier is missing. All PROV elements require a valid identifier.\nERROR cwltool:main.py:1380 Workflow error, try again with --debug for more information:\nAn identifier is missing. All PROV elements require a valid identifier.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 9375ad8418044ca8e4643e8f37ed017315fdf87f snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: fa1deaa87312d274883b86e302388f6ddc3905d61021690eebd4e480e2ed0722 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 4fa1b2b9ac92d356c9856c47a425afe6137c6db7273b4b9fd4f5b0e79b566aada35799132692bdfd96b5be15a54948849ab37bd8f85b0ee0fc48f1872195ba20 snapshot/revsort.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: e9c2cc242c5c8cc20d57f505891142e1382cf1a1 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 4328177d10e69f3d72c01b99921d70dce8c7b6ae54a1c099b22ddd28b3d91703 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 49dfa0543d1135ad9b0f0743f85741782da42a7af46f35aa8ec38b1c5301b98499385ea68290ff01eae38452990c88ddd48f538b3d0cecb81dfa205ccd38df02 snapshot/revtool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: da39a3ee5e6b4b0d3255bfef95601890afd80709 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e snapshot/empty.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 953b6a4167b2033182d5320ba8c885c5c6e92a39 snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: f8a8c32b27b9750e237470c5fe29f46a3fe248d64ed88c177e8a4798b5d6096d snapshot/sorttool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 5f007a093f75e3b59023d483ee7113c3fb0c82603829f936fb36c665bc40b3103a6b24316bf7cc42f6e7c7c9ddbe8edecefcc1390bde51c29366275c2d7c164f snapshot/sorttool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: d4e780eac6b995170c5544138e51cee42bf82b02 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 71854d40af17ddaad25710ff92bed3033edc5312cea32640d1780241b99df51f metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: ba634748b2a242590fe4f2f293ea32ab4cae028fc7ba9a83b3ce2964374030766b9b71e13fe231a9e27877e79b5c939c949ce2cab6806a002f4ef8005ea34504 metadata/logs/engine.345438a6-047a-4f43-85b9-ebfad1253d22.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: fa166224b2884b8c1a7019701241269f0fe8f4ba metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: b220ef2e9661453dc089f3645d905eb38ede5f81267288875ebaa393f440a3b6 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 67dc40c370f4eb425ad35887933493d90057b10fb0d6c65a7b9dd47fd482ce515036fe98304f7a6254891a4240f1f515e792dd7c3610f9d4e38c5954de185854 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha1.txt: 7b845a04531a0aea8b66445b3cb5dfd3cc38987e bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha256.txt: 674fc7391ca2a9c892cc4a7b8f6d69ef84f4debea78506708c389a4611090a94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu/tagmanifest-sha512.txt: 350e30ea50137627007116ea6a7b9e3f71a7b9e01835e5e0b82201f45bd7f577cc3f294c98401c2afabc72bd7c331d4a7ad8cb70dcac056749b3d897311a5e03 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/m6ftcecu\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_revsort_workflow_shortcut0/provenance')], 'duration': 0.0016798560000097496, 'start': 1685951459.699641, 'stop': 1685951459.701323, '$report_type': 'TestReport', 'item_index': 526, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_revsort_workflow_shortcut - location: ('tests/test_provenance.py', 85, 'test_revsort_workflow_shortcut') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_nested_workflow - location: ('tests/test_provenance.py', 98, 'test_nested_workflow') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_nested_workflow', 'location': ('tests/test_provenance.py', 98, 'test_nested_workflow'), 'keywords': {'test_nested_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018565800000942545, 'start': 1685951459.703209, 'stop': 1685951459.705068, '$report_type': 'TestReport', 'item_index': 527, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_stderr', 'location': ('tests/test_stdout_stderr_log_dir.py', 43, 'test_log_dir_echo_stderr'), 'keywords': {'test_log_dir_echo_stderr': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo-stderr.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo-stderr.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo-stderr.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo-stderr.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "echo $(inputs.message) 1>&2"\n }\n]\nDEBUG cwltool:job.py:215 [job echo-stderr.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job echo-stderr.cwl] /private/tmp/docker_tmpy47xscwu$ bash \\\n -c \\\n \'echo hello 1>&2\' 2> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_log_dir_echo_stderr0/echo-stderr.cwl/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo-stderr.cwl] completed success\nDEBUG cwltool:job.py:422 [job echo-stderr.cwl] outputs {\n "out": "hello\\n"\n}\nDEBUG cwltool:job.py:446 [job echo-stderr.cwl] Removing input staging directory /private/tmp/docker_tmpq05r80i_\nDEBUG cwltool:job.py:454 [job echo-stderr.cwl] Removing temporary directory /private/tmp/docker_tmpyd_d2wbt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpy47xscwu\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7239499830002387, 'start': 1685951459.06056, 'stop': 1685951459.7844942, '$report_type': 'TestReport', 'item_index': 597, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_stderr', 'location': ('tests/test_stdout_stderr_log_dir.py', 43, 'test_log_dir_echo_stderr'), 'keywords': {'test_log_dir_echo_stderr': 1, 'test_stdout_stderr_log_dir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job echo-stderr.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/echo-stderr.cwl\nDEBUG cwltool:command_line_tool.py:988 [job echo-stderr.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job echo-stderr.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job echo-stderr.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "bash"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-c"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "echo $(inputs.message) 1>&2"\n }\n]\nDEBUG cwltool:job.py:215 [job echo-stderr.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job echo-stderr.cwl] /private/tmp/docker_tmpy47xscwu$ bash \\\n -c \\\n \'echo hello 1>&2\' 2> /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_log_dir_echo_stderr0/echo-stderr.cwl/out.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job echo-stderr.cwl] completed success\nDEBUG cwltool:job.py:422 [job echo-stderr.cwl] outputs {\n "out": "hello\\n"\n}\nDEBUG cwltool:job.py:446 [job echo-stderr.cwl] Removing input staging directory /private/tmp/docker_tmpq05r80i_\nDEBUG cwltool:job.py:454 [job echo-stderr.cwl] Removing temporary directory /private/tmp/docker_tmpyd_d2wbt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpy47xscwu\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005019689997425303, 'start': 1685951459.785346, 'stop': 1685951459.785849, '$report_type': 'TestReport', 'item_index': 597, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_stdout_stderr_log_dir.py::test_log_dir_echo_stderr - location: ('tests/test_stdout_stderr_log_dir.py', 43, 'test_log_dir_echo_stderr') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_streaming.py::test_regular_file - location: ('tests/test_streaming.py', 47, 'test_regular_file') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_streaming.py::test_regular_file', 'location': ('tests/test_streaming.py', 47, 'test_regular_file'), 'keywords': {'test_regular_file': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003891579999617534, 'start': 1685951459.7871192, 'stop': 1685951459.78751, '$report_type': 'TestReport', 'item_index': 598, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_streaming.py::test_regular_file', 'location': ('tests/test_streaming.py', 47, 'test_regular_file'), 'keywords': {'test_regular_file': 1, 'test_streaming.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:50:59]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:10b10210-be50-4068-984c-fae3f949ab6d] initializing from 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<_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_streaming.py::test_input_can_be_named_pipe[True-True-False] - location: ('tests/test_streaming.py', 76, 'test_input_can_be_named_pipe[True-True-False]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_collision - location: ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_collision', 'location': ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision'), 'keywords': {'test_single_process_inherit_reqs_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014390340002137236, 'start': 1685951459.813792, 'stop': 1685951459.815232, '$report_type': 'TestReport', 'item_index': 613, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqshints', 'location': ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints'), 'keywords': {'test_single_process_inherit_reqshints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp1rf1mf2r$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp1rf1mf2r/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1rf1mf2r/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmpay9r1t0o\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmptl9zl9t0\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1rf1mf2r/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1rf1mf2r\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.823703552000552, 'start': 1685951459.3311412, 'stop': 1685951460.154825, '$report_type': 'TestReport', 'item_index': 611, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqshints', 'location': ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints'), 'keywords': {'test_single_process_inherit_reqshints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp1rf1mf2r$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp1rf1mf2r/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp1rf1mf2r/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmpay9r1t0o\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmptl9zl9t0\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp1rf1mf2r/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp1rf1mf2r\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000500224999996135, 'start': 1685951460.15571, 'stop': 1685951460.156211, '$report_type': 'TestReport', 'item_index': 611, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqshints - location: ('tests/test_subgraph.py', 91, 'test_single_process_inherit_reqshints') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision - location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_hints_collision', 'location': ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision'), 'keywords': {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018444249999447493, 'start': 1685951460.158337, 'stop': 1685951460.160183, '$report_type': 'TestReport', 'item_index': 612, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_get_subgraph_long_out_form', 'location': ('tests/test_subgraph.py', 55, 'test_get_subgraph_long_out_form'), 'keywords': {'test_get_subgraph_long_out_form': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', "WARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?")], 'duration': 0.9022642480003924, 'start': 1685951459.459401, 'stop': 1685951460.361644, '$report_type': 'TestReport', 'item_index': 609, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_get_subgraph_long_out_form', 'location': ('tests/test_subgraph.py', 55, 'test_get_subgraph_long_out_form'), 'keywords': {'test_get_subgraph_long_out_form': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?\n"), ('Captured log call', "WARNING salad:ref_resolver.py:240 URI prefix 'cwltool' of 'cwltool:loop' not recognized, are you missing a $namespaces section?")], 'duration': 0.00020006900012958795, 'start': 1685951460.362091, 'stop': 1685951460.362292, '$report_type': 'TestReport', 'item_index': 609, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_get_subgraph_long_out_form - location: ('tests/test_subgraph.py', 55, 'test_get_subgraph_long_out_form') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_get_step - location: ('tests/test_subgraph.py', 70, 'test_get_step') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_get_step', 'location': ('tests/test_subgraph.py', 70, 'test_get_step'), 'keywords': {'test_get_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003287249992354191, 'start': 1685951460.364289, 'stop': 1685951460.364619, '$report_type': 'TestReport', 'item_index': 610, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity.py::test_singularity_iwdr', 'location': ('tests/test_singularity.py', 62, 'test_singularity_iwdr'), 'keywords': {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:810 Singularity error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 771, in run\n self.get_from_requirements(\n File "/Users/jasperk/gitlab/cwltool/cwltool/singularity.py", line 292, in get_from_requirements\n raise WorkflowException("singularity executable is not available")\ncwltool.errors.WorkflowException: singularity executable is not available\nERROR cwltool:main.py:1373 Workflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available')], 'duration': 0.7381495270001324, 'start': 1685951459.641752, 'stop': 1685951460.379884, '$report_type': 'TestReport', 'item_index': 588, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity.py::test_singularity_iwdr', 'location': ('tests/test_singularity.py', 62, 'test_singularity_iwdr'), 'keywords': {'test_singularity_iwdr': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mWorkflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available\x1b[0m\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl",\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job iwdr-entry.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/iwdr-entry.cwl\nDEBUG cwltool:command_line_tool.py:988 [job iwdr-entry.cwl] {\n "message": "hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job iwdr-entry.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job iwdr-entry.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "example.conf"\n }\n]\nDEBUG cwltool:job.py:810 Singularity error\nTraceback (most recent call last):\n File "/Users/jasperk/gitlab/cwltool/cwltool/job.py", line 771, in run\n self.get_from_requirements(\n File "/Users/jasperk/gitlab/cwltool/cwltool/singularity.py", line 292, in get_from_requirements\n raise WorkflowException("singularity executable is not available")\ncwltool.errors.WorkflowException: singularity executable is not available\nERROR cwltool:main.py:1373 Workflow or tool uses unsupported feature:\nSingularity is required to run this tool: singularity executable is not available')], 'duration': 0.00043232999996689614, 'start': 1685951460.380364, 'stop': 1685951460.3807979, '$report_type': 'TestReport', 'item_index': 588, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_singularity.py::test_singularity_iwdr - location: ('tests/test_singularity.py', 62, 'test_singularity_iwdr') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull - location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity.py::test_singularity_incorrect_image_pull', 'location': ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull'), 'keywords': {'test_singularity_incorrect_image_pull': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 84, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00022189900028024567, 'start': 1685951460.381962, 'stop': 1685951460.382185, '$report_type': 'TestReport', 'item_index': 589, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity.py::test_singularity_incorrect_image_pull', 'location': ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull'), 'keywords': {'test_singularity_incorrect_image_pull': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00021053000000392785, 'start': 1685951460.382848, 'stop': 1685951460.38306, '$report_type': 'TestReport', 'item_index': 589, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_singularity.py::test_singularity_incorrect_image_pull - location: ('tests/test_singularity.py', 83, 'test_singularity_incorrect_image_pull') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_singularity.py::test_singularity_local - location: ('tests/test_singularity.py', 98, 'test_singularity_local') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity.py::test_singularity_local', 'location': ('tests/test_singularity.py', 98, 'test_singularity_local'), 'keywords': {'test_singularity_local': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'skipped', 'longrepr': ('/Users/jasperk/gitlab/cwltool/tests/test_singularity.py', 99, 'Skipped: Requires the singularity executable on the system path.'), 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002089989993692143, 'start': 1685951460.385066, 'stop': 1685951460.3852758, '$report_type': 'TestReport', 'item_index': 590, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('skipped', 's', 'SKIPPED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_singularity.py::test_singularity_local', 'location': ('tests/test_singularity.py', 98, 'test_singularity_local'), 'keywords': {'test_singularity_local': 1, 'skipif': 1, 'pytestmark': 1, 'test_singularity.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0002950230000351439, 'start': 1685951460.38608, 'stop': 1685951460.3863769, '$report_type': 'TestReport', 'item_index': 590, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_singularity.py::test_singularity_local - location: ('tests/test_singularity.py', 98, 'test_singularity_local') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step - location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_packed_subwf_step', 'location': ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step'), 'keywords': {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001556540999445133, 'start': 1685951460.3884459, 'stop': 1685951460.390004, '$report_type': 'TestReport', 'item_index': 618, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_get_step', 'location': ('tests/test_subgraph.py', 70, 'test_get_step'), 'keywords': {'test_get_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:00]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1\x1b[0m\n"), ('Captured log call', "WARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.1355143520004276, 'start': 1685951460.364971, 'stop': 1685951460.500483, '$report_type': 'TestReport', 'item_index': 610, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_get_step', 'location': ('tests/test_subgraph.py', 70, 'test_get_step'), 'keywords': {'test_get_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:00]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33mWorkflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1\x1b[0m\n"), ('Captured log call', "WARNING cwltool:checker.py:319 Workflow checker warning:\ntests/subgraph/count-lines1-wf.cwl:62:7: 'file3' is not an input parameter of\n file:///Users/jasperk/gitlab/cwltool/tests/subgraph/wc-tool.cwl,\n expected file1")], 'duration': 0.00021679000019503292, 'start': 1685951460.5012228, 'stop': 1685951460.501441, '$report_type': 'TestReport', 'item_index': 610, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_get_step - location: ('tests/test_subgraph.py', 70, 'test_get_step') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_subwf_step - location: ('tests/test_subgraph.py', 188, 'test_single_process_subwf_step') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_step', 'location': ('tests/test_subgraph.py', 188, 'test_single_process_subwf_step'), 'keywords': {'test_single_process_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001321605000157433, 'start': 1685951460.5035431, 'stop': 1685951460.5048661, '$report_type': 'TestReport', 'item_index': 617, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_collision', 'location': ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision'), 'keywords': {'test_single_process_inherit_reqs_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmp6nz6ufny$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp6nz6ufny/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6nz6ufny/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmp4ckaad43\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpzyry0m08\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6nz6ufny/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6nz6ufny\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.843506232999971, 'start': 1685951459.815787, 'stop': 1685951460.659273, '$report_type': 'TestReport', 'item_index': 613, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_collision', 'location': ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision'), 'keywords': {'test_single_process_inherit_reqs_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmp6nz6ufny$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp6nz6ufny/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6nz6ufny/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmp4ckaad43\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpzyry0m08\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6nz6ufny/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6nz6ufny\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006021980007062666, 'start': 1685951460.660255, 'stop': 1685951460.6608582, '$report_type': 'TestReport', 'item_index': 613, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_collision - location: ('tests/test_subgraph.py', 123, 'test_single_process_inherit_reqs_collision') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision - location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision', 'location': ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision'), 'keywords': {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014790080003876938, 'start': 1685951460.662613, 'stop': 1685951460.664093, '$report_type': 'TestReport', 'item_index': 614, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_hints_collision', 'location': ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision'), 'keywords': {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl_2] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl_2] /private/tmp/docker_tmp0rf0qbvp$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp0rf0qbvp/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp0rf0qbvp/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl_2] Removing input staging directory /private/tmp/docker_tmpun5mynhb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl_2] Removing temporary directory /private/tmp/docker_tmp2g3z32z6\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0rf0qbvp/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0rf0qbvp\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9018843539997761, 'start': 1685951460.1607418, 'stop': 1685951461.062607, '$report_type': 'TestReport', 'item_index': 612, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_hints_collision', 'location': ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision'), 'keywords': {'test_single_process_inherit_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl_2] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl_2] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl_2] /private/tmp/docker_tmp0rf0qbvp$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp0rf0qbvp/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl_2] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl_2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp0rf0qbvp/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl_2] Removing input staging directory /private/tmp/docker_tmpun5mynhb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl_2] Removing temporary directory /private/tmp/docker_tmp2g3z32z6\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0rf0qbvp/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_hi0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0rf0qbvp\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007875250003053225, 'start': 1685951461.064188, 'stop': 1685951461.064978, '$report_type': 'TestReport', 'item_index': 612, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_hints_collision - location: ('tests/test_subgraph.py', 107, 'test_single_process_inherit_hints_collision') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision - location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision', 'location': ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision'), 'keywords': {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0019690780000019004, 'start': 1685951461.066408, 'stop': 1685951461.068379, '$report_type': 'TestReport', 'item_index': 615, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names', 'location': ('tests/test_relocate.py', 20, 'test_for_conflict_file_names'), 'keywords': {'test_for_conflict_file_names': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] inputs {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step step1_5\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_5] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_6] /private/tmp/docker_tmp0419t2y2$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] Removing input staging directory /private/tmp/docker_tmpgggel8mc\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] Removing temporary directory /private/tmp/docker_tmpftf5rp4l\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step step2_4\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_4] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_4\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2] /private/tmp/docker_tmpbg5nbyyo$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] Removing input staging directory /private/tmp/docker_tmph0b3hrp3\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] Removing temporary directory /private/tmp/docker_tmpmhnabfu2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp0419t2y2/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpbg5nbyyo/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp7qi3ddmh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpbg5nbyyo\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp0419t2y2\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step step1_5\nDEBUG cwltool:workflow_job.py:727 [step step1_5] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1_5] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_5\nDEBUG cwltool:command_line_tool.py:988 [job step1_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_6] initial work dir {}\nINFO cwltool:job.py:266 [job step1_6] /private/tmp/docker_tmp0419t2y2$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_6] completed success\nDEBUG cwltool:job.py:422 [job step1_6] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_5] completed success\nDEBUG cwltool:job.py:446 [job step1_6] Removing input staging directory /private/tmp/docker_tmpgggel8mc\nDEBUG cwltool:job.py:454 [job step1_6] Removing temporary directory /private/tmp/docker_tmpftf5rp4l\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step step2_4\nDEBUG cwltool:workflow_job.py:727 [step step2_4] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step2_4] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step2_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_4\nDEBUG cwltool:command_line_tool.py:988 [job step2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step2] initial work dir {}\nINFO cwltool:job.py:266 [job step2] /private/tmp/docker_tmpbg5nbyyo$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step2] completed success\nDEBUG cwltool:job.py:422 [job step2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _7] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step2] Removing input staging directory /private/tmp/docker_tmph0b3hrp3\nDEBUG cwltool:job.py:454 [job step2] Removing temporary directory /private/tmp/docker_tmpmhnabfu2\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0419t2y2/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpbg5nbyyo/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7qi3ddmh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbg5nbyyo\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0419t2y2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.7811133960003644, 'start': 1685951459.571585, 'stop': 1685951461.352656, '$report_type': 'TestReport', 'item_index': 575, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names', 'location': ('tests/test_relocate.py', 20, 'test_for_conflict_file_names'), 'keywords': {'test_for_conflict_file_names': 1, 'skipif': 1, 'pytestmark': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] inputs {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step step1_5\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_5] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_6] /private/tmp/docker_tmp0419t2y2$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_6] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] Removing input staging directory /private/tmp/docker_tmpgggel8mc\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_6] Removing temporary directory /private/tmp/docker_tmpftf5rp4l\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _7] starting step step2_4\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_4] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_4\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2] /private/tmp/docker_tmpbg5nbyyo$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _7] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] Removing input staging directory /private/tmp/docker_tmph0b3hrp3\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2] Removing temporary directory /private/tmp/docker_tmpmhnabfu2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmp0419t2y2/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpbg5nbyyo/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp7qi3ddmh\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpbg5nbyyo\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmp0419t2y2\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _7] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _7] start\nDEBUG cwltool:workflow_job.py:777 [workflow _7] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step step1_5\nDEBUG cwltool:workflow_job.py:727 [step step1_5] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1_5] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_6] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_5\nDEBUG cwltool:command_line_tool.py:988 [job step1_6] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_6] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_6] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_6] initial work dir {}\nINFO cwltool:job.py:266 [job step1_6] /private/tmp/docker_tmp0419t2y2$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_6] completed success\nDEBUG cwltool:job.py:422 [job step1_6] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_5] completed success\nDEBUG cwltool:job.py:446 [job step1_6] Removing input staging directory /private/tmp/docker_tmpgggel8mc\nDEBUG cwltool:job.py:454 [job step1_6] Removing temporary directory /private/tmp/docker_tmpftf5rp4l\nINFO cwltool:workflow_job.py:613 [workflow _7] starting step step2_4\nDEBUG cwltool:workflow_job.py:727 [step step2_4] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step2_4] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step2_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_4\nDEBUG cwltool:command_line_tool.py:988 [job step2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step2] initial work dir {}\nINFO cwltool:job.py:266 [job step2] /private/tmp/docker_tmpbg5nbyyo$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step2] completed success\nDEBUG cwltool:job.py:422 [job step2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _7] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _7] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmp0419t2y2/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpbg5nbyyo/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step2] Removing input staging directory /private/tmp/docker_tmph0b3hrp3\nDEBUG cwltool:job.py:454 [job step2] Removing temporary directory /private/tmp/docker_tmpmhnabfu2\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0419t2y2/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpbg5nbyyo/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names0/bzz_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp7qi3ddmh\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpbg5nbyyo\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0419t2y2\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0011240349995205179, 'start': 1685951461.354667, 'stop': 1685951461.355793, '$report_type': 'TestReport', 'item_index': 575, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_relocate.py::test_for_conflict_file_names - location: ('tests/test_relocate.py', 20, 'test_for_conflict_file_names') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_relocate.py::test_for_conflict_file_names_nodocker - location: ('tests/test_relocate.py', 39, 'test_for_conflict_file_names_nodocker') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names_nodocker', 'location': ('tests/test_relocate.py', 39, 'test_for_conflict_file_names_nodocker'), 'keywords': {'test_for_conflict_file_names_nodocker': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.002268951000587549, 'start': 1685951461.3601532, 'stop': 1685951461.3624241, '$report_type': 'TestReport', 'item_index': 576, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_packed_subwf_step', 'location': ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step'), 'keywords': {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp65j863ig$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp65j863ig/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp65j863ig/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmp11jtljvb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpwn42k8_w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp65j863ig/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp65j863ig\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.1143909949996669, 'start': 1685951460.390568, 'stop': 1685951461.5049338, '$report_type': 'TestReport', 'item_index': 618, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_packed_subwf_step', 'location': ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step'), 'keywords': {'test_single_process_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmp65j863ig$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp65j863ig/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp65j863ig/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmp11jtljvb\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpwn42k8_w\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp65j863ig/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_packed_sub0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp65j863ig\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006726860001435853, 'start': 1685951461.506804, 'stop': 1685951461.507478, '$report_type': 'TestReport', 'item_index': 618, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_packed_subwf_step - location: ('tests/test_subgraph.py', 204, 'test_single_process_packed_subwf_step') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step - location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step', 'location': ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step'), 'keywords': {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0021509959997274564, 'start': 1685951461.510327, 'stop': 1685951461.512479, '$report_type': 'TestReport', 'item_index': 619, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_step', 'location': ('tests/test_subgraph.py', 188, 'test_single_process_subwf_step'), 'keywords': {'test_single_process_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmpv_7ba0am$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpv_7ba0am/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpv_7ba0am/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmprro2yksj\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpxjj4rbu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpv_7ba0am/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_single_process_subwf_step0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpv_7ba0am\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.123654173000432, 'start': 1685951460.505218, 'stop': 1685951461.628845, '$report_type': 'TestReport', 'item_index': 617, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_step', 'location': ('tests/test_subgraph.py', 188, 'test_single_process_subwf_step'), 'keywords': {'test_single_process_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2.cwl] /private/tmp/docker_tmpv_7ba0am$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpv_7ba0am/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpv_7ba0am/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",\n "size": 9,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2.cwl] Removing input staging directory /private/tmp/docker_tmprro2yksj\nDEBUG cwltool:job.py:454 [job env-tool2.cwl] Removing temporary directory /private/tmp/docker_tmpxjj4rbu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpv_7ba0am/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_single_process_subwf_step0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpv_7ba0am\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008459549999315641, 'start': 1685951461.630202, 'stop': 1685951461.6310499, '$report_type': 'TestReport', 'item_index': 617, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_subwf_step - location: ('tests/test_subgraph.py', 188, 'test_single_process_subwf_step') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_step_subwf_step - location: ('tests/test_subgraph.py', 239, 'test_single_step_subwf_step') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_step_subwf_step', 'location': ('tests/test_subgraph.py', 239, 'test_single_step_subwf_step'), 'keywords': {'test_single_step_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0019193019998056116, 'start': 1685951461.6342149, 'stop': 1685951461.636136, '$report_type': 'TestReport', 'item_index': 620, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision', 'location': ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision'), 'keywords': {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initializing from _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c\nDEBUG cwltool:command_line_tool.py:988 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "valueFrom": "$(runtime.cores)"\n }\n]\nDEBUG cwltool:job.py:215 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initial work dir {}\nINFO cwltool:job.py:266 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] /private/tmp/docker_tmp0kfy0hx0$ echo \\\n 1 > /private/tmp/docker_tmp0kfy0hx0/cores.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] completed success\nDEBUG cwltool:job.py:422 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp0kfy0hx0/cores.txt",\n "basename": "cores.txt",\n "nameroot": "cores",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing input staging directory /private/tmp/docker_tmpy2q4uxic\nDEBUG cwltool:job.py:454 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing temporary directory /private/tmp/docker_tmp3u7l8gu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0kfy0hx0/cores.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1/cores.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0kfy0hx0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0293492290002177, 'start': 1685951460.664522, 'stop': 1685951461.693847, '$report_type': 'TestReport', 'item_index': 614, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision', 'location': ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision'), 'keywords': {'test_single_process_inherit_reqs_step_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/subgraph/steplevel-resreq.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initializing from _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c\nDEBUG cwltool:command_line_tool.py:988 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] {}\nDEBUG cwltool:command_line_tool.py:1000 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "valueFrom": "$(runtime.cores)"\n }\n]\nDEBUG cwltool:job.py:215 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] initial work dir {}\nINFO cwltool:job.py:266 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] /private/tmp/docker_tmp0kfy0hx0$ echo \\\n 1 > /private/tmp/docker_tmp0kfy0hx0/cores.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] completed success\nDEBUG cwltool:job.py:422 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp0kfy0hx0/cores.txt",\n "basename": "cores.txt",\n "nameroot": "cores",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e",\n "size": 2,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing input staging directory /private/tmp/docker_tmpy2q4uxic\nDEBUG cwltool:job.py:454 [job _:ae7eb1d6-96e0-4ffb-813b-a0f5aaf4d39c] Removing temporary directory /private/tmp/docker_tmp3u7l8gu9\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp0kfy0hx0/cores.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_process_inherit_re1/cores.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp0kfy0hx0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005337309994501993, 'start': 1685951461.694844, 'stop': 1685951461.69538, '$report_type': 'TestReport', 'item_index': 614, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_step_collision - location: ('tests/test_subgraph.py', 139, 'test_single_process_inherit_reqs_step_collision') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out - location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_step_wfstep_long_out', 'location': ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out'), 'keywords': {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0026018169992312323, 'start': 1685951461.6975958, 'stop': 1685951461.7001998, '$report_type': 'TestReport', 'item_index': 621, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision', 'location': ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision'), 'keywords': {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmpug5wf1yr$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpug5wf1yr/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpug5wf1yr/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmpr2_osg12\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpdzs6emmt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpug5wf1yr/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpug5wf1yr\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0924644189999526, 'start': 1685951461.068767, 'stop': 1685951462.161207, '$report_type': 'TestReport', 'item_index': 615, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision', 'location': ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision'), 'keywords': {'test_single_process_inherit_reqs_hints_collision': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_hint_req_collision.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_req.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_req.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_req.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_req.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_req.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_req.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_req.cwl] /private/tmp/docker_tmpug5wf1yr$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpug5wf1yr/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_req.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_req.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpug5wf1yr/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_req.cwl] Removing input staging directory /private/tmp/docker_tmpr2_osg12\nDEBUG cwltool:job.py:454 [job env-tool2_req.cwl] Removing temporary directory /private/tmp/docker_tmpdzs6emmt\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpug5wf1yr/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_re1/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpug5wf1yr\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.001123591000578017, 'start': 1685951462.162127, 'stop': 1685951462.163251, '$report_type': 'TestReport', 'item_index': 615, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_reqs_hints_collision - location: ('tests/test_subgraph.py', 156, 'test_single_process_inherit_reqs_hints_collision') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints - location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_only_hints', 'location': ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints'), 'keywords': {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.001528846999462985, 'start': 1685951462.165597, 'stop': 1685951462.1671271, '$report_type': 'TestReport', 'item_index': 616, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_step_subwf_step', 'location': ('tests/test_subgraph.py', 239, 'test_single_step_subwf_step'), 'keywords': {'test_single_step_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _21] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\nINFO cwltool:workflow_job.py:765 [workflow _21] start\nDEBUG cwltool:workflow_job.py:777 [workflow _21] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _21] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpxgr4sqjt$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpxgr4sqjt/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _21] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _21] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpb9c06wtf\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7_g0pfz8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpxgr4sqjt/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_single_step_subwf_step0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvvs07dnp\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxgr4sqjt\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9564511730004597, 'start': 1685951461.6367, 'stop': 1685951462.593131, '$report_type': 'TestReport', 'item_index': 620, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_step_subwf_step', 'location': ('tests/test_subgraph.py', 239, 'test_single_step_subwf_step'), 'keywords': {'test_single_step_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _21] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl\nINFO cwltool:workflow_job.py:765 [workflow _21] start\nDEBUG cwltool:workflow_job.py:777 [workflow _21] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _21] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpxgr4sqjt$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpxgr4sqjt/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _21] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _21] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpxgr4sqjt/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpb9c06wtf\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7_g0pfz8\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpxgr4sqjt/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_single_step_subwf_step0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvvs07dnp\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxgr4sqjt\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007508689996029716, 'start': 1685951462.5947719, 'stop': 1685951462.595524, '$report_type': 'TestReport', 'item_index': 620, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_step_subwf_step - location: ('tests/test_subgraph.py', 239, 'test_single_step_subwf_step') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_step - location: ('tests/test_subgraph.py', 301, 'test_print_targets_embedded_step') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_print_targets_embedded_step', 'location': ('tests/test_subgraph.py', 301, 'test_print_targets_embedded_step'), 'keywords': {'test_print_targets_embedded_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003762910000659758, 'start': 1685951462.598204, 'stop': 1685951462.598583, '$report_type': 'TestReport', 'item_index': 624, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_step_wfstep_long_out', 'location': ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out'), 'keywords': {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmp_d17nob5$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp_d17nob5/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfmqmaczt\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7l3r954g\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_d17nob5/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnx7s_q9a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_d17nob5\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0173719809999966, 'start': 1685951461.700803, 'stop': 1685951462.7181509, '$report_type': 'TestReport', 'item_index': 621, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_step_wfstep_long_out', 'location': ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out'), 'keywords': {'test_single_step_wfstep_long_out': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf_b.cwl\'\nDEBUG cwltool:workflow_job.py:498 [workflow _3] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl\nINFO cwltool:workflow_job.py:765 [workflow _3] start\nDEBUG cwltool:workflow_job.py:777 [workflow _3] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _3] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmp_d17nob5$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp_d17nob5/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_long.cwl#step1/out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _3] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _3] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp_d17nob5/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmpfmqmaczt\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp7l3r954g\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_d17nob5/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_single_step_wfstep_long_o0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpnx7s_q9a\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_d17nob5\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00103417099944636, 'start': 1685951462.723277, 'stop': 1685951462.7243142, '$report_type': 'TestReport', 'item_index': 621, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_step_wfstep_long_out - location: ('tests/test_subgraph.py', 255, 'test_single_step_wfstep_long_out') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_reqsinherit - location: ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_print_targets_embedded_reqsinherit', 'location': ('tests/test_subgraph.py', 312, 'test_print_targets_embedded_reqsinherit'), 'keywords': {'test_print_targets_embedded_reqsinherit': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00034795999999914784, 'start': 1685951462.72735, 'stop': 1685951462.727699, '$report_type': 'TestReport', 'item_index': 625, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_only_hints', 'location': ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints'), 'keywords': {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_no_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_no_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_no_env.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_no_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_no_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_no_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_no_env.cwl] /private/tmp/docker_tmpvp0cy1ef$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpvp0cy1ef/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_no_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_no_env.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpvp0cy1ef/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$ab5f2a9add5f54622dde555ac8ae9a3000e5ee0a",\n "size": 26,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_no_env.cwl] Removing input staging directory /private/tmp/docker_tmp3ef9ddmc\nDEBUG cwltool:job.py:454 [job env-tool2_no_env.cwl] Removing temporary directory /private/tmp/docker_tmp8ts5h8fu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvp0cy1ef/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvp0cy1ef\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.9118393700000524, 'start': 1685951462.167519, 'stop': 1685951463.079338, '$report_type': 'TestReport', 'item_index': 616, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_inherit_only_hints', 'location': ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints'), 'keywords': {'test_single_process_inherit_only_hints': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_only_hint.cwl\'\nDEBUG cwltool:command_line_tool.py:982 [job env-tool2_no_env.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-tool2_no_env.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env-tool2_no_env.cwl] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job env-tool2_no_env.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env-tool2_no_env.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job env-tool2_no_env.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job env-tool2_no_env.cwl] /private/tmp/docker_tmpvp0cy1ef$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmpvp0cy1ef/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env-tool2_no_env.cwl] completed success\nDEBUG cwltool:job.py:422 [job env-tool2_no_env.cwl] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmpvp0cy1ef/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$ab5f2a9add5f54622dde555ac8ae9a3000e5ee0a",\n "size": 26,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job env-tool2_no_env.cwl] Removing input staging directory /private/tmp/docker_tmp3ef9ddmc\nDEBUG cwltool:job.py:454 [job env-tool2_no_env.cwl] Removing temporary directory /private/tmp/docker_tmp8ts5h8fu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpvp0cy1ef/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_single_process_inherit_on0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpvp0cy1ef\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0006480779993580654, 'start': 1685951463.08046, 'stop': 1685951463.08111, '$report_type': 'TestReport', 'item_index': 616, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_inherit_only_hints - location: ('tests/test_subgraph.py', 172, 'test_single_process_inherit_only_hints') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs - location: ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_print_targets_embedded_sub_subwfs', 'location': ('tests/test_subgraph.py', 323, 'test_print_targets_embedded_sub_subwfs'), 'keywords': {'test_print_targets_embedded_sub_subwfs': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003258949991504778, 'start': 1685951463.0834339, 'stop': 1685951463.083762, '$report_type': 'TestReport', 'item_index': 626, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names_nodocker', 'location': ('tests/test_relocate.py', 39, 'test_for_conflict_file_names_nodocker'), 'keywords': {'test_for_conflict_file_names_nodocker': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] inputs {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step step2_5\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_5] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2_2] /private/tmp/docker_tmpcelhvc2f$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] Removing input staging directory /private/tmp/docker_tmpb4fzhykd\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] Removing temporary directory /private/tmp/docker_tmpvx5y2bc8\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step step1_6\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_6] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_7] /private/tmp/docker_tmpsy87u4a4$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _8] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] Removing input staging directory /private/tmp/docker_tmpbe_5fs0a\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] Removing temporary directory /private/tmp/docker_tmpv42ahjpr\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpsy87u4a4/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpcelhvc2f/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpeqv1tcya\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpsy87u4a4\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpcelhvc2f\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _8] start\nDEBUG cwltool:workflow_job.py:777 [workflow _8] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step step2_5\nDEBUG cwltool:workflow_job.py:727 [step step2_5] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step2_5] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step2_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_5\nDEBUG cwltool:command_line_tool.py:988 [job step2_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step2_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step2_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step2_2] initial work dir {}\nINFO cwltool:job.py:266 [job step2_2] /private/tmp/docker_tmpcelhvc2f$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step2_2] completed success\nDEBUG cwltool:job.py:422 [job step2_2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2_5] completed success\nDEBUG cwltool:job.py:446 [job step2_2] Removing input staging directory /private/tmp/docker_tmpb4fzhykd\nDEBUG cwltool:job.py:454 [job step2_2] Removing temporary directory /private/tmp/docker_tmpvx5y2bc8\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step step1_6\nDEBUG cwltool:workflow_job.py:727 [step step1_6] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1_6] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1_6] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_6\nDEBUG cwltool:command_line_tool.py:988 [job step1_7] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_7] initial work dir {}\nINFO cwltool:job.py:266 [job step1_7] /private/tmp/docker_tmpsy87u4a4$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_7] completed success\nDEBUG cwltool:job.py:422 [job step1_7] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow _8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _8] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_7] Removing input staging directory /private/tmp/docker_tmpbe_5fs0a\nDEBUG cwltool:job.py:454 [job step1_7] Removing temporary directory /private/tmp/docker_tmpv42ahjpr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpsy87u4a4/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpcelhvc2f/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpeqv1tcya\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsy87u4a4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcelhvc2f\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.8410316479994435, 'start': 1685951461.363033, 'stop': 1685951463.20402, '$report_type': 'TestReport', 'item_index': 576, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_relocate.py::test_for_conflict_file_names_nodocker', 'location': ('tests/test_relocate.py', 39, 'test_for_conflict_file_names_nodocker'), 'keywords': {'test_for_conflict_file_names_nodocker': 1, 'test_relocate.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] inputs {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step step2_5\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_5] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_5\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2_2] /private/tmp/docker_tmpcelhvc2f$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step2_2] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step2_5] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] Removing input staging directory /private/tmp/docker_tmpb4fzhykd\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step2_2] Removing temporary directory /private/tmp/docker_tmpvx5y2bc8\x1b[0m\n\x1b[1;30mINFO\x1b[0m [workflow _8] starting step step1_6\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] job input {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] evaluated job input to {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_6] start\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_6\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] path mappings is {}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_7] /private/tmp/docker_tmpsy87u4a4$ touch \\\n bzz\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job step1_7] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[step step1_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [step step1_6] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _8] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[workflow _8] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] Removing input staging directory /private/tmp/docker_tmpbe_5fs0a\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job step1_7] Removing temporary directory /private/tmp/docker_tmpv42ahjpr\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpsy87u4a4/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpcelhvc2f/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz_2\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpeqv1tcya\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpsy87u4a4\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpcelhvc2f\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _8] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _8] start\nDEBUG cwltool:workflow_job.py:777 [workflow _8] inputs {}\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step step2_5\nDEBUG cwltool:workflow_job.py:727 [step step2_5] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step2_5] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step2_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step2_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step2_5\nDEBUG cwltool:command_line_tool.py:988 [job step2_2] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step2_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step2_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step2_2] initial work dir {}\nINFO cwltool:job.py:266 [job step2_2] /private/tmp/docker_tmpcelhvc2f$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step2_2] completed success\nDEBUG cwltool:job.py:422 [job step2_2] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step2_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step2/bzz": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step2_5] completed success\nDEBUG cwltool:job.py:446 [job step2_2] Removing input staging directory /private/tmp/docker_tmpb4fzhykd\nDEBUG cwltool:job.py:454 [job step2_2] Removing temporary directory /private/tmp/docker_tmpvx5y2bc8\nINFO cwltool:workflow_job.py:613 [workflow _8] starting step step1_6\nDEBUG cwltool:workflow_job.py:727 [step step1_6] job input {}\nDEBUG cwltool:workflow_job.py:732 [step step1_6] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step step1_6] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_7] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#makebzz as part of step step1_6\nDEBUG cwltool:command_line_tool.py:988 [job step1_7] {}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_7] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_7] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "bzz"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_7] initial work dir {}\nINFO cwltool:job.py:266 [job step1_7] /private/tmp/docker_tmpsy87u4a4$ touch \\\n bzz\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_7] completed success\nDEBUG cwltool:job.py:422 [job step1_7] outputs {\n "bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_6] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/conflict.cwl#main/step1/bzz": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_6] completed success\nINFO cwltool:workflow_job.py:539 [workflow _8] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _8] outputs {\n "b1": {\n "location": "file:///private/tmp/docker_tmpsy87u4a4/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n },\n "b2": {\n "location": "file:///private/tmp/docker_tmpcelhvc2f/bzz",\n "basename": "bzz",\n "nameroot": "bzz",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_7] Removing input staging directory /private/tmp/docker_tmpbe_5fs0a\nDEBUG cwltool:job.py:454 [job step1_7] Removing temporary directory /private/tmp/docker_tmpv42ahjpr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpsy87u4a4/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpcelhvc2f/bzz to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_for_conflict_file_names_n0/bzz_2\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpeqv1tcya\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpsy87u4a4\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpcelhvc2f\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008877540003595641, 'start': 1685951463.20895, 'stop': 1685951463.20984, '$report_type': 'TestReport', 'item_index': 576, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_relocate.py::test_for_conflict_file_names_nodocker - location: ('tests/test_relocate.py', 39, 'test_for_conflict_file_names_nodocker') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_step_packed_subwf_step - location: ('tests/test_subgraph.py', 271, 'test_single_step_packed_subwf_step') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_step_packed_subwf_step', 'location': ('tests/test_subgraph.py', 271, 'test_single_step_packed_subwf_step'), 'keywords': {'test_single_step_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0015094909995241323, 'start': 1685951463.213248, 'stop': 1685951463.2147589, '$report_type': 'TestReport', 'item_index': 622, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_print_targets_embedded_step', 'location': ('tests/test_subgraph.py', 301, 'test_print_targets_embedded_step'), 'keywords': {'test_print_targets_embedded_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/timelimit2-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/timelimit2-wf.cwl'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:924 Input targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 step1 Output targets:\nINFO cwltool:main.py:924 step1 Input targets:\nINFO cwltool:main.py:924 step2 Output targets:\nINFO cwltool:main.py:924 step2 Input targets:")], 'duration': 0.8990280979996896, 'start': 1685951462.599144, 'stop': 1685951463.4981508, '$report_type': 'TestReport', 'item_index': 624, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_print_targets_embedded_step', 'location': ('tests/test_subgraph.py', 301, 'test_print_targets_embedded_step'), 'keywords': {'test_print_targets_embedded_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/subgraph/timelimit2-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/timelimit2-wf.cwl'\nINFO cwltool:main.py:924 Output targets:\nINFO cwltool:main.py:924 Input targets:\nINFO cwltool:main.py:933 steps targets:\nINFO cwltool:main.py:924 step1 Output targets:\nINFO cwltool:main.py:924 step1 Input targets:\nINFO cwltool:main.py:924 step2 Output targets:\nINFO cwltool:main.py:924 step2 Input targets:")], 'duration': 0.00032098200063046534, 'start': 1685951463.498822, 'stop': 1685951463.4991438, '$report_type': 'TestReport', 'item_index': 624, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_print_targets_embedded_step - location: ('tests/test_subgraph.py', 301, 'test_print_targets_embedded_step') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_target.py::test_target - location: ('tests/test_target.py', 5, 'test_target') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_target.py::test_target', 'location': ('tests/test_target.py', 5, 'test_target'), 'keywords': {'test_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002446250000502914, 'start': 1685951463.50105, 'stop': 1685951463.501296, '$report_type': 'TestReport', 'item_index': 627, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step', 'location': ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step'), 'keywords': {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\'\nDEBUG cwltool:command_line_tool.py:982 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json#count-lines17-wf/step1/run/count-lines17-wf.cwl@step_step1@run/stepX/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run/stepY/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run\nDEBUG cwltool:command_line_tool.py:988 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initial work dir {}\nINFO cwltool:job.py:266 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] /private/tmp/docker_tmp_9yt0z8_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_9yt0z8_,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmprz9dykzk,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpsbmfwops/20230605095102-600646.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt > /private/tmp/docker_tmp_9yt0z8_/output\nINFO cwltool:job.py:905 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] completed success\nDEBUG cwltool:job.py:422 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_9yt0z8_/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing input staging directory /private/tmp/docker_tmp89udep8a\nDEBUG cwltool:job.py:454 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing temporary directory /private/tmp/docker_tmprz9dykzk\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_9yt0z8_/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_9yt0z8_\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 2.11600468800043, 'start': 1685951461.5130591, 'stop': 1685951463.6290119, '$report_type': 'TestReport', 'item_index': 619, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step', 'location': ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step'), 'keywords': {'test_single_process_subwf_subwf_inline_step': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json\'\nDEBUG cwltool:command_line_tool.py:982 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/count-lines17-wf.cwl.json#count-lines17-wf/step1/run/count-lines17-wf.cwl@step_step1@run/stepX/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run/stepY/run/count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run\nDEBUG cwltool:command_line_tool.py:988 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] {\n "file1": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "size": 1111,\n "basename": "whale.txt",\n "nameroot": "whale",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/whale.txt": [\n "/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt",\n "/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "wc"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-l"\n }\n]\nDEBUG cwltool:job.py:215 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] initial work dir {}\nINFO cwltool:job.py:266 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] /private/tmp/docker_tmp_9yt0z8_$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp_9yt0z8_,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmprz9dykzk,target=/tmp \\\n --mount=type=bind,source=/Users/jasperk/gitlab/cwltool/tests/wf/whale.txt,target=/var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt,readonly \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --net=none \\\n --log-driver=none \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpsbmfwops/20230605095102-600646.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/debian:stable-slim \\\n wc \\\n -l < /var/lib/cwl/stg94bc421f-2ad5-4b5e-b6a2-57938736ff6e/whale.txt > /private/tmp/docker_tmp_9yt0z8_/output\nINFO cwltool:job.py:905 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] completed success\nDEBUG cwltool:job.py:422 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmp_9yt0z8_/output",\n "basename": "output",\n "nameroot": "output",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$3596ea087bfdaf52380eae441077572ed289d657",\n "size": 3,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing input staging directory /private/tmp/docker_tmp89udep8a\nDEBUG cwltool:job.py:454 [job count-lines17-wf.cwl@step_step1@run@step_stepX@run@step_stepY@run] Removing temporary directory /private/tmp/docker_tmprz9dykzk\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp_9yt0z8_/output to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_single_process_subwf_subw0/output\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp_9yt0z8_\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0008782109998719534, 'start': 1685951463.630854, 'stop': 1685951463.6317341, '$report_type': 'TestReport', 'item_index': 619, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_process_subwf_subwf_inline_step - location: ('tests/test_subgraph.py', 220, 'test_single_process_subwf_subwf_inline_step') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value - location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_with_step_level_default_value', 'location': ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value'), 'keywords': {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00043156799983989913, 'start': 1685951463.634976, 'stop': 1685951463.6354098, '$report_type': 'TestReport', 'item_index': 623, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_step_packed_subwf_step', 'location': ('tests/test_subgraph.py', 271, 'test_single_step_packed_subwf_step'), 'keywords': {'test_single_step_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "tests/subgraph/env-wf2_subwf-packed.cwl:71:29: object id 'tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in' previously defined\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nWARNING salad:ref_resolver.py:1130 tests/subgraph/env-wf2_subwf-packed.cwl:71:29: object id \'tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step step1_7\nDEBUG cwltool:workflow_job.py:727 [step step1_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_7] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl as part of step step1_7\nDEBUG cwltool:command_line_tool.py:988 [job step1_8] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_8] initial work dir {}\nINFO cwltool:job.py:266 [job step1_8] /private/tmp/docker_tmp6xo49icl$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp6xo49icl/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_8] completed success\nDEBUG cwltool:job.py:422 [job step1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow _9] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_8] Removing input staging directory /private/tmp/docker_tmp9x013gp5\nDEBUG cwltool:job.py:454 [job step1_8] Removing temporary directory /private/tmp/docker_tmpga8veylr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6xo49icl/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_single_step_packed_subwf_0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6xo49icl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp12rf8g5q\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.0249070469999424, 'start': 1685951463.215264, 'stop': 1685951464.240148, '$report_type': 'TestReport', 'item_index': 622, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_step_packed_subwf_step', 'location': ('tests/test_subgraph.py', 271, 'test_single_step_packed_subwf_step'), 'keywords': {'test_single_step_packed_subwf_step': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "tests/subgraph/env-wf2_subwf-packed.cwl:71:29: object id 'tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in' previously defined\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\'\nWARNING salad:ref_resolver.py:1130 tests/subgraph/env-wf2_subwf-packed.cwl:71:29: object id \'tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in\' previously defined\nDEBUG cwltool:workflow_job.py:498 [workflow _9] initialized from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl\nINFO cwltool:workflow_job.py:765 [workflow _9] start\nDEBUG cwltool:workflow_job.py:777 [workflow _9] inputs {\n "in": "hello test env"\n}\nINFO cwltool:workflow_job.py:613 [workflow _9] starting step step1_7\nDEBUG cwltool:workflow_job.py:727 [step step1_7] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in": "hello test env"\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_7] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/in": "hello test env"\n}\nINFO cwltool:workflow_job.py:75 [step step1_7] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_8] initializing from file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-tool2.cwl as part of step step1_7\nDEBUG cwltool:command_line_tool.py:988 [job step1_8] {\n "in": "hello test env"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_8] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_8] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "/bin/sh"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "-c"\n },\n {\n "position": [\n -1000000,\n 2\n ],\n "datum": "echo $TEST_ENV"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_8] initial work dir {}\nINFO cwltool:job.py:266 [job step1_8] /private/tmp/docker_tmp6xo49icl$ /bin/sh \\\n -c \\\n \'echo $TEST_ENV\' > /private/tmp/docker_tmp6xo49icl/out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_8] completed success\nDEBUG cwltool:job.py:422 [job step1_8] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_7] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/subgraph/env-wf2_subwf-packed.cwl#env-wf2.cwl/step1/out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nINFO cwltool:workflow_job.py:572 [step step1_7] completed success\nINFO cwltool:workflow_job.py:539 [workflow _9] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _9] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp6xo49icl/out",\n "basename": "out",\n "nameroot": "out",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c",\n "size": 15,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job step1_8] Removing input staging directory /private/tmp/docker_tmp9x013gp5\nDEBUG cwltool:job.py:454 [job step1_8] Removing temporary directory /private/tmp/docker_tmpga8veylr\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmp6xo49icl/out to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_single_step_packed_subwf_0/out\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp6xo49icl\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp12rf8g5q\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0007419650000883848, 'start': 1685951464.2413802, 'stop': 1685951464.242124, '$report_type': 'TestReport', 'item_index': 622, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_step_packed_subwf_step - location: ('tests/test_subgraph.py', 271, 'test_single_step_packed_subwf_step') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_tmpdir.py::test_docker_commandLineTool_job_tmpdir_prefix - location: ('tests/test_tmpdir.py', 26, 'test_docker_commandLineTool_job_tmpdir_prefix') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_tmpdir.py::test_docker_commandLineTool_job_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 26, 'test_docker_commandLineTool_job_tmpdir_prefix'), 'keywords': {'test_docker_commandLineTool_job_tmpdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0018374299997958587, 'start': 1685951464.2446148, 'stop': 1685951464.246454, '$report_type': 'TestReport', 'item_index': 630, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_tmpdir.py::test_docker_commandLineTool_job_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 26, 'test_docker_commandLineTool_job_tmpdir_prefix'), 'keywords': {'test_docker_commandLineTool_job_tmpdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[32m[2023-06-05 09:51:04]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:654967f3-fadf-4ec8-acdb-74060e241e57] initializing from _:654967f3-fadf-4ec8-acdb-74060e241e57\x1b[0m\n\x1b[32m[2023-06-05 09:51:04]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:654967f3-fadf-4ec8-acdb-74060e241e57] {}\x1b[0m\n\x1b[32m[2023-06-05 09:51:04]\x1b[0m \x1b[1;30mDEBUG\x1b[0m \x1b[32m[job _:654967f3-fadf-4ec8-acdb-74060e241e57] path mappings is 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enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 74ece951469a5306ac6512cff2a9f3b25b91c858 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: a0f6fb34d0ba97018b294486569ded02bb6e6e659d3e06c5de4f214582691f36 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: f0dca2f20d6e9cd7b5ca6e9ea53e3c5548164e2b77ca0b2a1f3e785ce12f314ca29d1943f80ee974373ab7ead0031aee08c07bb511c34c82cc951e3bef28c9b0 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _18] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile not ready\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step create-tar\nDEBUG cwltool:workflow_job.py:727 [step create-tar] job input {}\nDEBUG cwltool:workflow_job.py:732 [step create-tar] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step create-tar] start\nDEBUG cwltool:command_line_tool.py:982 [job create-tar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/fbd87079-fe0c-4de9-b99f-0c79323cf2c1 as part of step create-tar\nDEBUG cwltool:command_line_tool.py:988 [job create-tar] {}\nDEBUG cwltool:command_line_tool.py:1000 [job create-tar] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job create-tar] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "date\\ntar cf hello.tar Hello.java\\ndate\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job create-tar] initial work dir {\n "_:5de9498b-d23e-4bbf-b5e6-3d9459eedb80": [\n "public class Hello {\\n public static void main(String[] argv) {\\n System.out.println(\\"Hello from Java\\");\\n }\\n}\\n",\n "/private/tmp/docker_tmpkyipo8y7/Hello.java",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 4864f67aab6874db8b656c7b15bd7cfc595e9571 data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nINFO cwltool:job.py:419 [job create-tar] completed success\nDEBUG cwltool:job.py:422 [job create-tar] outputs {\n "tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step create-tar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:572 [step create-tar] completed success\nDEBUG cwltool:job.py:446 [job create-tar] Removing input staging directory /private/tmp/docker_tmpzx57hfi5\nDEBUG cwltool:job.py:454 [job create-tar] Removing temporary directory /private/tmp/docker_tmp4rtd4n2g\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step compile\nDEBUG cwltool:workflow_job.py:727 [step compile] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step compile] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step compile] start\nDEBUG cwltool:workflow_job.py:498 [workflow compile] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow compile] start\nDEBUG cwltool:workflow_job.py:777 [workflow compile] inputs {\n "ex": "Hello.java",\n "inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:610 [workflow compile] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument not ready\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step untar\nDEBUG cwltool:workflow_job.py:727 [step untar] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step untar] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step untar] start\nDEBUG cwltool:command_line_tool.py:982 [job untar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/tar-param.cwl as part of step untar\nDEBUG cwltool:command_line_tool.py:988 [job untar] {\n "extractfile": "Hello.java",\n "tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job untar] path mappings is {\n "file:///private/tmp/docker_tmpkyipo8y7/hello.tar": [\n "/private/tmp/docker_tmpkyipo8y7/hello.tar",\n "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job untar] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "tar"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "xf"\n },\n {\n "position": [\n 1,\n "tarfile"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9",\n "path": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "dirname": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134"\n }\n },\n {\n "position": [\n 2,\n "extractfile"\n ],\n "datum": "Hello.java"\n }\n]\nDEBUG cwltool:job.py:215 [job untar] initial work dir {}\nINFO cwltool:job.py:266 [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 93035905e94e150874f5a881d39f3c5c6378dd38 data/93/93035905e94e150874f5a881d39f3c5c6378dd38\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nINFO cwltool:job.py:419 [job untar] completed success\nDEBUG cwltool:job.py:422 [job untar] outputs {\n "example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step untar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step untar] completed success\nDEBUG cwltool:job.py:446 [job untar] Removing input staging directory /private/tmp/docker_tmp8uve11w8\nDEBUG cwltool:job.py:454 [job untar] Removing temporary directory /private/tmp/docker_tmpnpvtosz9\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step argument\nDEBUG cwltool:workflow_job.py:727 [step argument] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step argument] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:75 [step argument] start\nDEBUG cwltool:command_line_tool.py:982 [job argument] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/arguments.cwl as part of step argument\nDEBUG cwltool:command_line_tool.py:988 [job argument] {\n "src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job argument] path mappings is {\n "file:///private/tmp/docker_tmpc_ieg46p/Hello.java": [\n "/private/tmp/docker_tmpc_ieg46p/Hello.java",\n "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job argument] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "javac"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-d"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(runtime.outdir)"\n },\n {\n "position": [\n 1,\n "src"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5",\n "path": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "dirname": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/openjdk:9.0.1-11-slim\']\nDEBUG cwltool:job.py:215 [job argument] initial work dir {}\nINFO cwltool:job.py:266 [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\nINFO cwltool:job.py:905 [job argument] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 39e3219327347c05aa3e82236f83aa6d77fe6bfd data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nINFO cwltool:job.py:419 [job argument] completed success\nDEBUG cwltool:job.py:422 [job argument] outputs {\n "classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step argument] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step argument] completed success\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 83049fca7761d12fb0a5da48da3c037c5304a0fc metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 60258aab9b1b640774e4705795ed3f7ae538c98238f3fae97911d4b93bbfaa2d metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 33139ea057934520ce5f2525af14fafb879322770000acdb150ee5aa445568f3588850a5f5951dce7a03937af0e4ae1ecddafaff17b8299b4e9b2d2372aa07e7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0304d4e8c149fbe870496f20f4c073b6946f7fe7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 13120ba16180324a0c690989fede01b2424adce87145cd0da6492b177f8f814c metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 86e81f57bbb1e5335d9dd2921076dfeba39e953bc4214261e7d818a3a7f38ebb9c4367320cf6fa2714c96e00132009d102c6b6604f36fefc1639cdb722d70715 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: cff4ad2216ea628f4975c69699c8e3fc0c3e4632 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 5d742295d8aba73c67424e366c394e0a34f773985c1645c9b6910e35e353afc9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c6b20c2741a3fa0edeb70054d7f72885b90dd62331b41d5f9fb9f2032495d78b83428995111a6ba52d098f57d976c760321811e6ea182d2e2f562976ba5ad1c9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 1fdf97a3b214d0a050db07a554ecfe44b056e655 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 325d75d9f711a5a12feee43188da250d5fdc200b6ca2e33214209fed193a87c8 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8cac58c921bd6a7115ef1dace866bdb2b84dd948cbed5014ab70eae79abe7b30e8ddeafc033659ddb581ac53550230aa818e3623fc55cebae094df17b7b9cd64 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9f2ad16a37a1df641dfe180c8704e88211c46676 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 939e5a54c9079007e36c852408057047622c11cb1d06b2b64b82636d8a1d6762 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 65707a62469cf55e9dcb8fdfe87bf1af958df3846a5de0a6c4732557af5ad6ddfd07fae87e80e7c4c3cef36d0b3b25b03293a5805ddeecf1d86980a7bff1e885 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9be8dfc973c5248324d388bda772ced2eafc5d09 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 4ad66e5bea19ad398ad45267244c6fb7e950340d509df851edbad2fbb844a504 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 63e5b105c46bef759931359c5994f6cff8029bb8a59911a3458df8d1e4e1b98fb3b6f8689c2096670880e2833bd3ae7e369b8e77ef0c7ae613edb86ff6dd9887 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nINFO cwltool:workflow_job.py:539 [workflow compile] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow compile] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step compile] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step compile] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:job.py:446 [job argument] Removing input staging directory /private/tmp/docker_tmpebe5z0v8\nDEBUG cwltool:job.py:454 [job argument] Removing temporary directory /private/tmp/docker_tmpdff4tkfu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpepzg_f_c/Hello.class to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzrpr1a4o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr_sgrnnb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpepzg_f_c\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkyipo8y7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpc_ieg46p\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 19fbff09cc97d57d7241305ed0cb03212f211ae9 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 410b6c9c1c10cc229c8781ddc5074f25f371cdf9b4e6e053758e98931db2f7eb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 6c75e7c3ef6bf96b917b3961bf1350658fec598fb67d194716c7fa281d09ae834cf81cea64f8636e34b2a8391b8d4391e267b526d90b3460ed50ffa35b615b9f metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 42906be32350038218f034e2418bfa414323fecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 54d1a6a2ea333664645b1ef510288b473b2798d0eba102c7d9f83979acdb30ea metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 59de6004ed6286c5bf4461690f1eea3eecec94be8cf7f186aa9100dd447ed2d3f8e78d8bb9a09b712d6bf0c16f036559fb76f2e57f9c9bf47f5b868d5a5b1698 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 54936279704d89dd038e6bb6207276b94ccf52c7 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48a6d44504c674c65ae71bf0186c051343568e8b1796272af0adf58b39dfc015 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 77323c4d9ca07d91bcb9db9f7090422963c30ec31c9cc7312a2619f60dfb0f8632630019a19f57fd3f2bbe2a354d0328dfb60c482f81141a31ea1b3c118e2466 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 76273be200ec2c229e213509b9bb670478dce7f4 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48244946e314f094d1b6c4b6e30a3358b5cbca006e442806c064eb0ffb961c1a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 64a2901aa5304fa5d65408f3a61b12c9131f251d89f4e688f9c3c3cdcba700f7fc67069606af5b24e6196f60e2553a53f51fda4ff970d89a7d91881ff5ffc4b5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: d80b34fd80aa3f9137314feb7021908e2b52cb91 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cc95cb90e86609a55c17cd318a3e5bd9892687cc6df9ba66fc8479dfd0d95aef metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 697c8c7b70137288a5672502d3786e77f04ce6f28f5a549ac71edb9f8bac64d7cb6ee4ef13ce84d9184f865db3ccaa66cf20bc62f31824e4b558a9bb959d6ef4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: f8b1b468869ac1a80043e092868c2277f1d15c64 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1805212079569e9a572fab9cdb3b73665e98e5ca3ec88d9b637ee30ffd026e11 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 036d8f071535a67857917407770951d720c444f3b9057b0bd8194be89066977bcc223f1ad268b552ea07d143c886679c4cbb66d79a0dea214672d54ec41358ff metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'classout\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello.class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 419\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a77f1bf715803e410ab8646eec4bee4f620aca8f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 023017d52b11f799321c82c33eb3f4b053ed57872618d37d30b69ec0c64902f8 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8e911b78c78b0a5146fc24f8adbdf1f253a2d78f6239c81533b0166ebd4f7ed7dd64e7fb3f86a7f62eb6d4288ade648629ef6c28ad1ab4accadc2800a8038123 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 724b068a51d129c5492f28865b3bed0eb22a8dec snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 0727286ce68bebcae06f0cb1da28a58382c9db14f0e4eae7e29f5644483d16cb snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c116c653cd68a7fd934d7df77d24a4977efa1c6505d6c32b138aec44130d40228f7d69bf3b11fb9473e421755e7d592f15b1aa93c988b1ec3249dc84139b7960 snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 7b997f5397fd668969634a4e8c113cec0fbbc5e8 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cdd580b6c0f37c60cc39ef4968184235ade6ab7369329b363c5db7f101f6d3a4 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 3c72796915141289f4e94ec0b83fa5fbd0203d8afb69adf0dcd866a616ddc9a432d071e75e54f3eafcd3d850411b6cfb54643cf123fb246206f49885a0b5fdbf snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b9b609b8713bd5ebed4e83e8074f84648a5f6708 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 6ddc89e25e65a9a6e80de48be06442cef0128b9f1c82ec8d50019223c5bfd866 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 58e44c861533f86faee277fc618bd869781ec5c1203bad37d150dd5efaed44d51198c9fed40ddd62b9ef348e2a9b9f5004d86c9983ee22ac61070b0c588a8229 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a11e6ae3b6824babd50ca5a96395030d203565f6 snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ba73050af0d17a6a24d82aeb88b54150e38189056007f1dd094a59562f30475d snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 57fe970c776bf2b8f283783b6565d886acd7f5974ec7a7a9de547201585a93130c40b494e29bb2a489123dc5d0c30f791c585f1f29dc11ff8d381b16c7d9e348 snapshot/tar-param.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0dd82b60f74970af2204ec209f5d9ba9bcf90ab1 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1991adaba7d0cdd01efb884f896e70162a678d6c019c8af40a628e3e81c958dd metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c8b1f27a515fda5fffc55d93abf31ae91d00fe9077046e16109522c83fd5740e4df390bb7dce1e8d7c5ee00e3d1532e298ee248addec8623f2d88f1f0b5d94d4 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b201b1900b531a5cac833222efcf2ea148ee8e4f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: be90e3007275188cbc913e1d8e0b2901a70917ecb0c4d82a9967a894ad18fc33 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca20cd4c002dea5a664c54c7a7d874ed07461ed50baf0016e4e9c45fdaa16132772748146c0f39bf409004e80e3c2ee9db16490543e86a8e41e45cea5758d3af metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 8e62f08782410be5f7a325ad891118c1c8b048c9 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: af35cf1992cf37219396ab2b24f2c0bc89e1e9d3fa27c63d3f8c8a2a64c2b62a bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c3bdb2ec78cc257d15b637073d81804b259e9bd197b9b0aa71d9a3b66b7eee0df29dbd0f6146ebdb9fee6e3adc073a09a3cd260708cc7890a982c547bb28d165 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance')], 'duration': 5.002003371999308, 'start': 1685951459.705703, 'stop': 1685951464.707586, '$report_type': 'TestReport', 'item_index': 527, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_nested_workflow', 'location': ('tests/test_provenance.py', 98, 'test_nested_workflow'), 'keywords': {'test_nested_workflow': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "classout": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class",\n "basename": "Hello.class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class"\n }\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [workflow _18] start\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step create-tar\n\x1b[1;30mINFO\x1b[0m [step create-tar] start\n\x1b[1;30mINFO\x1b[0m [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nMon Jun 5 09:51:00 CEST 2023\nMon Jun 5 09:51:00 CEST 2023\n\x1b[1;30mINFO\x1b[0m [job create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [step create-tar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] starting step compile\n\x1b[1;30mINFO\x1b[0m [step compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] start\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step untar\n\x1b[1;30mINFO\x1b[0m [step untar] start\n\x1b[1;30mINFO\x1b[0m [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\n\x1b[1;30mINFO\x1b[0m [job untar] completed success\n\x1b[1;30mINFO\x1b[0m [step untar] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] starting step argument\n\x1b[1;30mINFO\x1b[0m [step argument] start\n\x1b[1;30mINFO\x1b[0m ['docker', 'pull', 'docker.io/openjdk:9.0.1-11-slim']\n9.0.1-11-slim: Pulling from library/openjdk\nDigest: sha256:dc239c9a17aa509d4e79dc4980e40a5f0c8af78a9bcefab2b5eedf819f702298\nStatus: Image is up to date for openjdk:9.0.1-11-slim\ndocker.io/library/openjdk:9.0.1-11-slim\n\x1b[1;30mINFO\x1b[0m [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\n\x1b[1;30mINFO\x1b[0m [job argument] Max memory used: 0MiB\n\x1b[1;30mINFO\x1b[0m [job argument] completed success\n\x1b[1;30mINFO\x1b[0m [step argument] completed success\n\x1b[1;30mINFO\x1b[0m [workflow compile] completed success\n\x1b[1;30mINFO\x1b[0m [step compile] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _18] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\', job_order=[])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 74ece951469a5306ac6512cff2a9f3b25b91c858 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: a0f6fb34d0ba97018b294486569ded02bb6e6e659d3e06c5de4f214582691f36 workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: f0dca2f20d6e9cd7b5ca6e9ea53e3c5548164e2b77ca0b2a1f3e785ce12f314ca29d1943f80ee974373ab7ead0031aee08c07bb511c34c82cc951e3bef28c9b0 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpe3qqpvoo/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl"\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {}\nDEBUG cwltool:workflow_job.py:610 [workflow _18] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile not ready\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step create-tar\nDEBUG cwltool:workflow_job.py:727 [step create-tar] job input {}\nDEBUG cwltool:workflow_job.py:732 [step create-tar] evaluated job input to {}\nINFO cwltool:workflow_job.py:75 [step create-tar] start\nDEBUG cwltool:command_line_tool.py:982 [job create-tar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/fbd87079-fe0c-4de9-b99f-0c79323cf2c1 as part of step create-tar\nDEBUG cwltool:command_line_tool.py:988 [job create-tar] {}\nDEBUG cwltool:command_line_tool.py:1000 [job create-tar] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job create-tar] command line bindings is [\n {\n "shellQuote": false,\n "valueFrom": "date\\ntar cf hello.tar Hello.java\\ndate\\n",\n "position": [\n 0,\n 0\n ]\n }\n]\nDEBUG cwltool:job.py:215 [job create-tar] initial work dir {\n "_:5de9498b-d23e-4bbf-b5e6-3d9459eedb80": [\n "public class Hello {\\n public static void main(String[] argv) {\\n System.out.println(\\"Hello from Java\\");\\n }\\n}\\n",\n "/private/tmp/docker_tmpkyipo8y7/Hello.java",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job create-tar] /private/tmp/docker_tmpkyipo8y7$ /bin/sh \\\n -c \\\n date\ntar cf hello.tar Hello.java\ndate\n\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 4864f67aab6874db8b656c7b15bd7cfc595e9571 data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/48/4864f67aab6874db8b656c7b15bd7cfc595e9571\nINFO cwltool:job.py:419 [job create-tar] completed success\nDEBUG cwltool:job.py:422 [job create-tar] outputs {\n "tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step create-tar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#create-tar/tar": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:572 [step create-tar] completed success\nDEBUG cwltool:job.py:446 [job create-tar] Removing input staging directory /private/tmp/docker_tmpzx57hfi5\nDEBUG cwltool:job.py:454 [job create-tar] Removing temporary directory /private/tmp/docker_tmp4rtd4n2g\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step compile\nDEBUG cwltool:workflow_job.py:727 [step compile] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step compile] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/ex": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step compile] start\nDEBUG cwltool:workflow_job.py:498 [workflow compile] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow compile] start\nDEBUG cwltool:workflow_job.py:777 [workflow compile] inputs {\n "ex": "Hello.java",\n "inp": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:610 [workflow compile] job step file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument not ready\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step untar\nDEBUG cwltool:workflow_job.py:727 [step untar] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step untar] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/extractfile": "Hello.java",\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nINFO cwltool:workflow_job.py:75 [step untar] start\nDEBUG cwltool:command_line_tool.py:982 [job untar] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/tar-param.cwl as part of step untar\nDEBUG cwltool:command_line_tool.py:988 [job untar] {\n "extractfile": "Hello.java",\n "tarfile": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job untar] path mappings is {\n "file:///private/tmp/docker_tmpkyipo8y7/hello.tar": [\n "/private/tmp/docker_tmpkyipo8y7/hello.tar",\n "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job untar] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "tar"\n },\n {\n "position": [\n -1000000,\n 1\n ],\n "datum": "xf"\n },\n {\n "position": [\n 1,\n "tarfile"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpkyipo8y7/hello.tar",\n "basename": "hello.tar",\n "nameroot": "hello",\n "nameext": ".tar",\n "class": "File",\n "checksum": "sha1$4864f67aab6874db8b656c7b15bd7cfc595e9571",\n "size": 2048,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:8cf4c38a-b683-4d42-8ce2-1198afc7ebc9",\n "path": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar",\n "dirname": "/private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134"\n }\n },\n {\n "position": [\n 2,\n "extractfile"\n ],\n "datum": "Hello.java"\n }\n]\nDEBUG cwltool:job.py:215 [job untar] initial work dir {}\nINFO cwltool:job.py:266 [job untar] /private/tmp/docker_tmpc_ieg46p$ tar \\\n xf \\\n /private/tmp/docker_tmp8uve11w8/stga360008f-2880-471f-849b-cc546f844134/hello.tar \\\n Hello.java\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/eb/eb07afb8bc2f3dceff34c8a8e82e5fe716819d6f\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 93035905e94e150874f5a881d39f3c5c6378dd38 data/93/93035905e94e150874f5a881d39f3c5c6378dd38\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/93/93035905e94e150874f5a881d39f3c5c6378dd38\nINFO cwltool:job.py:419 [job untar] completed success\nDEBUG cwltool:job.py:422 [job untar] outputs {\n "example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step untar] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#untar/example_out": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:572 [step untar] completed success\nDEBUG cwltool:job.py:446 [job untar] Removing input staging directory /private/tmp/docker_tmp8uve11w8\nDEBUG cwltool:job.py:454 [job untar] Removing temporary directory /private/tmp/docker_tmpnpvtosz9\nINFO cwltool:workflow_job.py:613 [workflow compile] starting step argument\nDEBUG cwltool:workflow_job.py:727 [step argument] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step argument] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nINFO cwltool:workflow_job.py:75 [step argument] start\nDEBUG cwltool:command_line_tool.py:982 [job argument] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/arguments.cwl as part of step argument\nDEBUG cwltool:command_line_tool.py:988 [job argument] {\n "src": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job argument] path mappings is {\n "file:///private/tmp/docker_tmpc_ieg46p/Hello.java": [\n "/private/tmp/docker_tmpc_ieg46p/Hello.java",\n "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job argument] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "javac"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-d"\n },\n {\n "position": [\n 0,\n 1\n ],\n "valueFrom": "$(runtime.outdir)"\n },\n {\n "position": [\n 1,\n "src"\n ],\n "datum": {\n "location": "file:///private/tmp/docker_tmpc_ieg46p/Hello.java",\n "basename": "Hello.java",\n "nameroot": "Hello",\n "nameext": ".java",\n "class": "File",\n "checksum": "sha1$93035905e94e150874f5a881d39f3c5c6378dd38",\n "size": 115,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:fc427310-95f4-4034-9d74-6c1a0fb7b5b5",\n "path": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java",\n "dirname": "/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679"\n }\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/openjdk:9.0.1-11-slim\']\nDEBUG cwltool:job.py:215 [job argument] initial work dir {}\nINFO cwltool:job.py:266 [job argument] /private/tmp/docker_tmpepzg_f_c$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmpepzg_f_c,target=/gpLUSy \\\n --mount=type=bind,source=/private/tmp/docker_tmpdff4tkfu,target=/tmp \\\n --mount=type=bind,source=/private/tmp/docker_tmpc_ieg46p/Hello.java,target=/var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java,readonly \\\n --workdir=/gpLUSy \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmp2jf2gjtq/20230605095102-543269.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/gpLUSy \\\n docker.io/openjdk:9.0.1-11-slim \\\n javac \\\n -d \\\n /gpLUSy \\\n /var/lib/cwl/stg08334ad8-e617-43d2-a4fb-cdce7c7f6679/Hello.java\nINFO cwltool:job.py:905 [job argument] Max memory used: 0MiB\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/manifest-sha1.txt: 39e3219327347c05aa3e82236f83aa6d77fe6bfd data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nINFO cwltool:job.py:419 [job argument] completed success\nDEBUG cwltool:job.py:422 [job argument] outputs {\n "classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step argument] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/1st-workflow.cwl#argument/classfile": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step argument] completed success\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 83049fca7761d12fb0a5da48da3c037c5304a0fc metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 60258aab9b1b640774e4705795ed3f7ae538c98238f3fae97911d4b93bbfaa2d metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 33139ea057934520ce5f2525af14fafb879322770000acdb150ee5aa445568f3588850a5f5951dce7a03937af0e4ae1ecddafaff17b8299b4e9b2d2372aa07e7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0304d4e8c149fbe870496f20f4c073b6946f7fe7 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 13120ba16180324a0c690989fede01b2424adce87145cd0da6492b177f8f814c metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 86e81f57bbb1e5335d9dd2921076dfeba39e953bc4214261e7d818a3a7f38ebb9c4367320cf6fa2714c96e00132009d102c6b6604f36fefc1639cdb722d70715 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: cff4ad2216ea628f4975c69699c8e3fc0c3e4632 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 5d742295d8aba73c67424e366c394e0a34f773985c1645c9b6910e35e353afc9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c6b20c2741a3fa0edeb70054d7f72885b90dd62331b41d5f9fb9f2032495d78b83428995111a6ba52d098f57d976c760321811e6ea182d2e2f562976ba5ad1c9 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 1fdf97a3b214d0a050db07a554ecfe44b056e655 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 325d75d9f711a5a12feee43188da250d5fdc200b6ca2e33214209fed193a87c8 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8cac58c921bd6a7115ef1dace866bdb2b84dd948cbed5014ab70eae79abe7b30e8ddeafc033659ddb581ac53550230aa818e3623fc55cebae094df17b7b9cd64 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9f2ad16a37a1df641dfe180c8704e88211c46676 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 939e5a54c9079007e36c852408057047622c11cb1d06b2b64b82636d8a1d6762 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 65707a62469cf55e9dcb8fdfe87bf1af958df3846a5de0a6c4732557af5ad6ddfd07fae87e80e7c4c3cef36d0b3b25b03293a5805ddeecf1d86980a7bff1e885 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 9be8dfc973c5248324d388bda772ced2eafc5d09 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 4ad66e5bea19ad398ad45267244c6fb7e950340d509df851edbad2fbb844a504 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 63e5b105c46bef759931359c5994f6cff8029bb8a59911a3458df8d1e4e1b98fb3b6f8689c2096670880e2833bd3ae7e369b8e77ef0c7ae613edb86ff6dd9887 metadata/provenance/workflow_20compile.b283bb0c-ea9a-483c-8437-83a43764d4d8.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nINFO cwltool:workflow_job.py:539 [workflow compile] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow compile] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step compile] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/nested.cwl#compile/classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nINFO cwltool:workflow_job.py:572 [step compile] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {\n "classout": {\n "location": "file:///private/tmp/docker_tmpepzg_f_c/Hello.class",\n "basename": "Hello.class",\n "nameroot": "Hello",\n "nameext": ".class",\n "class": "File",\n "checksum": "sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd",\n "size": 419,\n "http://commonwl.org/cwltool#generation": 0,\n "@id": "urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974"\n }\n}\nDEBUG cwltool:job.py:446 [job argument] Removing input staging directory /private/tmp/docker_tmpebe5z0v8\nDEBUG cwltool:job.py:454 [job argument] Removing temporary directory /private/tmp/docker_tmpdff4tkfu\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpepzg_f_c/Hello.class to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzrpr1a4o\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpr_sgrnnb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpepzg_f_c\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpkyipo8y7\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpc_ieg46p\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 19fbff09cc97d57d7241305ed0cb03212f211ae9 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 410b6c9c1c10cc229c8781ddc5074f25f371cdf9b4e6e053758e98931db2f7eb metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 6c75e7c3ef6bf96b917b3961bf1350658fec598fb67d194716c7fa281d09ae834cf81cea64f8636e34b2a8391b8d4391e267b526d90b3460ed50ffa35b615b9f metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 42906be32350038218f034e2418bfa414323fecc metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 54d1a6a2ea333664645b1ef510288b473b2798d0eba102c7d9f83979acdb30ea metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 59de6004ed6286c5bf4461690f1eea3eecec94be8cf7f186aa9100dd447ed2d3f8e78d8bb9a09b712d6bf0c16f036559fb76f2e57f9c9bf47f5b868d5a5b1698 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 54936279704d89dd038e6bb6207276b94ccf52c7 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48a6d44504c674c65ae71bf0186c051343568e8b1796272af0adf58b39dfc015 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 77323c4d9ca07d91bcb9db9f7090422963c30ec31c9cc7312a2619f60dfb0f8632630019a19f57fd3f2bbe2a354d0328dfb60c482f81141a31ea1b3c118e2466 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 76273be200ec2c229e213509b9bb670478dce7f4 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 48244946e314f094d1b6c4b6e30a3358b5cbca006e442806c064eb0ffb961c1a metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 64a2901aa5304fa5d65408f3a61b12c9131f251d89f4e688f9c3c3cdcba700f7fc67069606af5b24e6196f60e2553a53f51fda4ff970d89a7d91881ff5ffc4b5 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: d80b34fd80aa3f9137314feb7021908e2b52cb91 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cc95cb90e86609a55c17cd318a3e5bd9892687cc6df9ba66fc8479dfd0d95aef metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 697c8c7b70137288a5672502d3786e77f04ce6f28f5a549ac71edb9f8bac64d7cb6ee4ef13ce84d9184f865db3ccaa66cf20bc62f31824e4b558a9bb959d6ef4 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: f8b1b468869ac1a80043e092868c2277f1d15c64 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1805212079569e9a572fab9cdb3b73665e98e5ca3ec88d9b637ee30ffd026e11 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 036d8f071535a67857917407770951d720c444f3b9057b0bd8194be89066977bcc223f1ad268b552ea07d143c886679c4cbb66d79a0dea214672d54ec41358ff metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'classout\': {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/cwltool-run/Hello.class\', \'basename\': \'Hello.class\', \'nameroot\': \'Hello\', \'nameext\': \'.class\', \'class\': \'File\', \'checksum\': \'sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\', \'size\': 419, \'http://commonwl.org/cwltool#generation\': 0, \'@id\': \'urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\'}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/39/39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello.class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: Hello\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .class\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 419\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 0\nDEBUG cwltool:ro.py:591 [provenance] Relativising: urn:uuid:c9cb1c39-8d1f-464d-a98f-403cb2a5c974\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a77f1bf715803e410ab8646eec4bee4f620aca8f workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 023017d52b11f799321c82c33eb3f4b053ed57872618d37d30b69ec0c64902f8 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 8e911b78c78b0a5146fc24f8adbdf1f253a2d78f6239c81533b0166ebd4f7ed7dd64e7fb3f86a7f62eb6d4288ade648629ef6c28ad1ab4accadc2800a8038123 workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 724b068a51d129c5492f28865b3bed0eb22a8dec snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 0727286ce68bebcae06f0cb1da28a58382c9db14f0e4eae7e29f5644483d16cb snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c116c653cd68a7fd934d7df77d24a4977efa1c6505d6c32b138aec44130d40228f7d69bf3b11fb9473e421755e7d592f15b1aa93c988b1ec3249dc84139b7960 snapshot/nested.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 7b997f5397fd668969634a4e8c113cec0fbbc5e8 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: cdd580b6c0f37c60cc39ef4968184235ade6ab7369329b363c5db7f101f6d3a4 snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 3c72796915141289f4e94ec0b83fa5fbd0203d8afb69adf0dcd866a616ddc9a432d071e75e54f3eafcd3d850411b6cfb54643cf123fb246206f49885a0b5fdbf snapshot/1st-workflow.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b9b609b8713bd5ebed4e83e8074f84648a5f6708 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 6ddc89e25e65a9a6e80de48be06442cef0128b9f1c82ec8d50019223c5bfd866 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 58e44c861533f86faee277fc618bd869781ec5c1203bad37d150dd5efaed44d51198c9fed40ddd62b9ef348e2a9b9f5004d86c9983ee22ac61070b0c588a8229 snapshot/arguments.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: a11e6ae3b6824babd50ca5a96395030d203565f6 snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: ba73050af0d17a6a24d82aeb88b54150e38189056007f1dd094a59562f30475d snapshot/tar-param.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: 57fe970c776bf2b8f283783b6565d886acd7f5974ec7a7a9de547201585a93130c40b494e29bb2a489123dc5d0c30f791c585f1f29dc11ff8d381b16c7d9e348 snapshot/tar-param.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 0dd82b60f74970af2204ec209f5d9ba9bcf90ab1 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: 1991adaba7d0cdd01efb884f896e70162a678d6c019c8af40a628e3e81c958dd metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c8b1f27a515fda5fffc55d93abf31ae91d00fe9077046e16109522c83fd5740e4df390bb7dce1e8d7c5ee00e3d1532e298ee248addec8623f2d88f1f0b5d94d4 metadata/logs/engine.afb18554-0b15-4fd8-887e-b3bffb0b930f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: b201b1900b531a5cac833222efcf2ea148ee8e4f metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: be90e3007275188cbc913e1d8e0b2901a70917ecb0c4d82a9967a894ad18fc33 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: ca20cd4c002dea5a664c54c7a7d874ed07461ed50baf0016e4e9c45fdaa16132772748146c0f39bf409004e80e3c2ee9db16490543e86a8e41e45cea5758d3af metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha1.txt: 8e62f08782410be5f7a325ad891118c1c8b048c9 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha256.txt: af35cf1992cf37219396ab2b24f2c0bc89e1e9d3fa27c63d3f8c8a2a64c2b62a bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf/tagmanifest-sha512.txt: c3bdb2ec78cc257d15b637073d81804b259e9bd197b9b0aa71d9a3b66b7eee0df29dbd0f6146ebdb9fee6e3adc073a09a3cd260708cc7890a982c547bb28d165 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/gr2uf2wf\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_nested_workflow0/provenance')], 'duration': 0.00113051800053654, 'start': 1685951464.710773, 'stop': 1685951464.711905, '$report_type': 'TestReport', 'item_index': 527, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_nested_workflow - location: ('tests/test_provenance.py', 98, 'test_nested_workflow') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - when: runtest - nodeid: tests/test_provenance.py::test_nested_workflow - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_secondary_files_implicit - location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_implicit', 'location': ('tests/test_provenance.py', 103, 'test_secondary_files_implicit'), 'keywords': {'test_secondary_files_implicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0012492460000430583, 'start': 1685951464.7161531, 'stop': 1685951464.717403, '$report_type': 'TestReport', 'item_index': 528, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_tmpdir.py::test_remove_tmpdirs', 'location': ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs'), 'keywords': {'test_remove_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nHello\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello"\n }\n]\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/2yfuzdes\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/a2i94b9v\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6808559439996316, 'start': 1685951464.298953, 'stop': 1685951464.979794, '$report_type': 'TestReport', 'item_index': 636, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_tmpdir.py::test_remove_tmpdirs', 'location': ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs'), 'keywords': {'test_remove_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl'\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nHello\n\x1b[1;30mINFO\x1b[0m [job hello_single_tool.cwl] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl",\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:982 [job hello_single_tool.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/hello_single_tool.cwl\nDEBUG cwltool:command_line_tool.py:988 [job hello_single_tool.cwl] {\n "message": "Hello"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job hello_single_tool.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job hello_single_tool.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "Hello"\n }\n]\nDEBUG cwltool:job.py:215 [job hello_single_tool.cwl] initial work dir {}\nINFO cwltool:job.py:266 [job hello_single_tool.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz$ echo \\\n Hello\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job hello_single_tool.cwl] completed success\nDEBUG cwltool:job.py:422 [job hello_single_tool.cwl] outputs {}\nDEBUG cwltool:job.py:446 [job hello_single_tool.cwl] Removing input staging directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/2yfuzdes\nDEBUG cwltool:job.py:454 [job hello_single_tool.cwl] Removing temporary directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/a2i94b9v\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_remove_tmpdirs0/pklidwsz\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005884539996259264, 'start': 1685951464.980832, 'stop': 1685951464.9814222, '$report_type': 'TestReport', 'item_index': 636, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_tmpdir.py::test_remove_tmpdirs - location: ('tests/test_tmpdir.py', 261, 'test_remove_tmpdirs') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_tmpdir.py::test_leave_tmpdirs - location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_tmpdir.py::test_leave_tmpdirs', 'location': ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs'), 'keywords': {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016575850004301174, 'start': 1685951464.983828, 'stop': 1685951464.9854872, '$report_type': 'TestReport', 'item_index': 637, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_target.py::test_target', 'location': ('tests/test_target.py', 5, 'test_target'), 'keywords': {'test_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _22] start\n\x1b[1;30mINFO\x1b[0m [workflow _22] starting step step1_5\n\x1b[1;30mINFO\x1b[0m [step step1_5] start\n\x1b[1;30mINFO\x1b[0m [job step1_4] /private/tmp/docker_tmpzwwa6z6d$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpzwwa6z6d/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_4] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _22] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _22] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _22] start\nDEBUG cwltool:workflow_job.py:777 [workflow _22] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _22] starting step step1_5\nINFO cwltool:workflow_job.py:75 [step step1_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_5\nDEBUG cwltool:command_line_tool.py:988 [job step1_4] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_4] initial work dir {}\nINFO cwltool:job.py:266 [job step1_4] /private/tmp/docker_tmpzwwa6z6d$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpzwwa6z6d/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_4] completed success\nDEBUG cwltool:job.py:422 [job step1_4] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow _22] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _22] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_4] Removing input staging directory /private/tmp/docker_tmpr5xvimrj\nDEBUG cwltool:job.py:454 [job step1_4] Removing temporary directory /private/tmp/docker_tmpk8t9sgbi\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpd528_x8e\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzwwa6z6d\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.602284578999388, 'start': 1685951463.50167, 'stop': 1685951465.103916, '$report_type': 'TestReport', 'item_index': 627, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_target.py::test_target', 'location': ('tests/test_target.py', 5, 'test_target'), 'keywords': {'test_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mINFO\x1b[0m [workflow _22] start\n\x1b[1;30mINFO\x1b[0m [workflow _22] starting step step1_5\n\x1b[1;30mINFO\x1b[0m [step step1_5] start\n\x1b[1;30mINFO\x1b[0m [job step1_4] /private/tmp/docker_tmpzwwa6z6d$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpzwwa6z6d/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_4] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_5] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _22] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _22] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main\nINFO cwltool:workflow_job.py:765 [workflow _22] start\nDEBUG cwltool:workflow_job.py:777 [workflow _22] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _22] starting step step1_5\nINFO cwltool:workflow_job.py:75 [step step1_5] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_4] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#echo as part of step step1_5\nDEBUG cwltool:command_line_tool.py:988 [job step1_4] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_4] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_4] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_4] initial work dir {}\nINFO cwltool:job.py:266 [job step1_4] /private/tmp/docker_tmpzwwa6z6d$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpzwwa6z6d/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_4] completed success\nDEBUG cwltool:job.py:422 [job step1_4] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_5] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_5] completed success\nINFO cwltool:workflow_job.py:539 [workflow _22] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _22] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_4] Removing input staging directory /private/tmp/docker_tmpr5xvimrj\nDEBUG cwltool:job.py:454 [job step1_4] Removing temporary directory /private/tmp/docker_tmpk8t9sgbi\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpd528_x8e\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpzwwa6z6d\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005301219998727902, 'start': 1685951465.1055648, 'stop': 1685951465.106097, '$report_type': 'TestReport', 'item_index': 627, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_target.py::test_target - location: ('tests/test_target.py', 5, 'test_target') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_tmpdir.py::test_commandLineTool_job_tmpdir_prefix - location: ('tests/test_tmpdir.py', 71, 'test_commandLineTool_job_tmpdir_prefix') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_tmpdir.py::test_commandLineTool_job_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 71, 'test_commandLineTool_job_tmpdir_prefix'), 'keywords': {'test_commandLineTool_job_tmpdir_prefix': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0016978080002445495, 'start': 1685951465.108722, 'stop': 1685951465.1104221, '$report_type': 'TestReport', 'item_index': 631, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish 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file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'--file1\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl",\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt"\n }\n}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\', \'size\': 3, \'basename\': \'foo1.txt\', \'nameroot\': \'foo1\', \'nameext\': \'.txt\', \'secondaryFiles\': [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7fbe1688c021dd47067816cb1915f194a21b192a workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: fdd353f2fc1a5ce060db48433d4c5d39841c3a16a7b3859ecf40c5d0559585cb workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5af67683ddcf0dc25317f9299432e1b480cba92fefc530bb82144c0b46d090163964253480d1d2b57d8d93bc800be27c6a17552dff8d5d285dfea3792633143a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_3] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx",\n "size": 3\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpwlagwb74\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpneari7wr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmprjpz3kex\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm23vbaqp\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b4bef5453619901d1f8f99b5ae6de84b0d9e639b metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 5db39cc34f5ff26b64a03b03b9101fecc2312db65289fe2d1be735727992d8bd metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 8d283d305c0e6d11608b05d9a5e1ba5a75fb4aba75402c34b62e6d7daa1524e3e4995c7b5b7dd09e2e1b461a78c125bc27d82023ed600a5efe3ca285ad10ea97 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 8727ee5875ce1f873aaea8acd610451c6f552485 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 7ea7c1f314778c5b956cac5c77bce95ea6b88611ebbc7066030f869d1db4451d metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: bfc8b1282a1fb06945d4fe7918b05d4f0406bbf7cb97de9e7fc3a34a9d24662816b96a4494d9a1063a86717119f908eb3bf90fe45fe4ef1c346c31b9266615c3 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 137c02dbe6b251a0db3df717988e236021b8999b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 563c5a34f521209ac347f8053149f64041ee7b452c394b4d8c04be39be52d09c metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 2eb1f8f6df902d2db5dab2f042daad6a2b591ba84f6017b4920c49d9a72328f2c0e3b8624a9d3b4740645ab3df6fcbfea29f90b796df9be09a37cf9d455769dc metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: f958ba8327cc8b9af11b209e763c08fd828c4aae metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9eee73bac677248e20e3fdc1b3945afaa24f84f31779a432ecc800f5959ac994 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 98aff7bc546d9f42dfcb7cfc86031061cd09819e93cafb46dea0818f5f55023540eed22292a07e8cbee2e3b5a0a3da1b5096d16a38d308112c5b359c4a7e66ef metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 28ac6c4bb8ee879415c09c5c428f9e146863163b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd2b49ac8dce047e8c28351499fefd31d5acd14bd37d5bbb2a984b091accd35d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5a11c7149e3fe38c8365859626f63e90a4a2edbd1603d17ab341ef329bbe5a0b5408df2f612212175eec6fef219878b2cd631e8924ff2f66fab9df76f87a5d2b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 52e03863abba9f946950a2419bc5a3c9d593fd04 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 8e79daf03e3958103d27e310d0879c8812989df38d007346f55fb9433c4108c8 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 00f022778fd2a8b71a936a2bb5b382645d9663735588b29c3a4228989d43026867c3654b71a7087b9bdd09ebcdf95d5e97d22cabef6d0404bff05a436c15996b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 4b5fce360bf0db096420ddf360cb05fb63abef9a metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 12c59130a589553031e8a732559d20225da263aa19d2b43b4f23f2ff47a13396 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: a0f2b7ecf70b39b1e7b84ddab845455bf81f04019ecf1810b9540809be18cfb5a5fcdeb90986c4b11d0d86c85d38ced387beb5248a97e75460019687346cca41 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7da08c3bcf057f5790aae85a316cc4c7e84e8dae metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9822a8bb8f23ff4a5f546df0e1901dac8ce404c90cc9e864c932e858f342296c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 20961f19fd0db8bf533ce8aa98d561c15d672364183fc007e488c01e40271698363b6d1e35edfd4d109b9863391b666e44cb49cbec572343804ee8aec795de28 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3a83e9297c5eca6e6de723837360f84464d4ee94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 57f04fd3cbd44703b65a45ec0acd6b1e56243dd599476dff375f2c868198939d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 7eca04aa9b2734f1b61e65c7f009cd6ddd45735a0c303dd0653b766f411e9fdea1255c5db384dd0b3f787f5b1920fbacdea475948ad439ac70e2589a09f42b46 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance')], 'duration': 1.082738922000317, 'start': 1685951464.7178009, 'stop': 1685951465.800514, '$report_type': 'TestReport', 'item_index': 528, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_implicit', 'location': ('tests/test_provenance.py', 103, 'test_secondary_files_implicit'), 'keywords': {'test_secondary_files_implicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpoast9syc/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\n\x1b[1;30mINFO\x1b[0m [workflow _19] start\n\x1b[1;30mINFO\x1b[0m [workflow _19] starting step step1_3\n\x1b[1;30mINFO\x1b[0m [step step1_3] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _19] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl --file1 /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'--file1\', \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to 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File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\', \'basename\': \'foo1.txt.idx\', \'class\': \'File\', \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7fbe1688c021dd47067816cb1915f194a21b192a workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: fdd353f2fc1a5ce060db48433d4c5d39841c3a16a7b3859ecf40c5d0559585cb workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5af67683ddcf0dc25317f9299432e1b480cba92fefc530bb82144c0b46d090163964253480d1d2b57d8d93bc800be27c6a17552dff8d5d285dfea3792633143a workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _19] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nINFO cwltool:workflow_job.py:765 [workflow _19] start\nDEBUG cwltool:workflow_job.py:777 [workflow _19] inputs {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ]\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _19] starting step step1_3\nDEBUG cwltool:workflow_job.py:727 [step step1_3] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": 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cwltool:workflow_job.py:75 [step step1_3] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_3\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "file1": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "size": 3,\n "basename": "foo1.txt",\n "nameroot": "foo1",\n "nameext": ".txt",\n "secondaryFiles": [\n {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "basename": "foo1.txt.idx",\n "class": "File",\n "nameroot": "foo1.txt",\n "nameext": ".idx",\n "size": 3\n }\n ]\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/foo1.txt.idx",\n "/private/tmp/docker_tmpwlagwb74/stg5b1d949c-b3f6-49b4-97c1-6e1483324785/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpm23vbaqp$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_3] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_3] completed success\nINFO cwltool:workflow_job.py:539 [workflow _19] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _19] outputs {}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmpwlagwb74\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpneari7wr\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmprjpz3kex\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpm23vbaqp\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b4bef5453619901d1f8f99b5ae6de84b0d9e639b metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 5db39cc34f5ff26b64a03b03b9101fecc2312db65289fe2d1be735727992d8bd metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 8d283d305c0e6d11608b05d9a5e1ba5a75fb4aba75402c34b62e6d7daa1524e3e4995c7b5b7dd09e2e1b461a78c125bc27d82023ed600a5efe3ca285ad10ea97 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 8727ee5875ce1f873aaea8acd610451c6f552485 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 7ea7c1f314778c5b956cac5c77bce95ea6b88611ebbc7066030f869d1db4451d metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: bfc8b1282a1fb06945d4fe7918b05d4f0406bbf7cb97de9e7fc3a34a9d24662816b96a4494d9a1063a86717119f908eb3bf90fe45fe4ef1c346c31b9266615c3 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 137c02dbe6b251a0db3df717988e236021b8999b metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 563c5a34f521209ac347f8053149f64041ee7b452c394b4d8c04be39be52d09c metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 2eb1f8f6df902d2db5dab2f042daad6a2b591ba84f6017b4920c49d9a72328f2c0e3b8624a9d3b4740645ab3df6fcbfea29f90b796df9be09a37cf9d455769dc metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: f958ba8327cc8b9af11b209e763c08fd828c4aae metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9eee73bac677248e20e3fdc1b3945afaa24f84f31779a432ecc800f5959ac994 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 98aff7bc546d9f42dfcb7cfc86031061cd09819e93cafb46dea0818f5f55023540eed22292a07e8cbee2e3b5a0a3da1b5096d16a38d308112c5b359c4a7e66ef metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 28ac6c4bb8ee879415c09c5c428f9e146863163b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd2b49ac8dce047e8c28351499fefd31d5acd14bd37d5bbb2a984b091accd35d metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 5a11c7149e3fe38c8365859626f63e90a4a2edbd1603d17ab341ef329bbe5a0b5408df2f612212175eec6fef219878b2cd631e8924ff2f66fab9df76f87a5d2b metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 52e03863abba9f946950a2419bc5a3c9d593fd04 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 8e79daf03e3958103d27e310d0879c8812989df38d007346f55fb9433c4108c8 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 00f022778fd2a8b71a936a2bb5b382645d9663735588b29c3a4228989d43026867c3654b71a7087b9bdd09ebcdf95d5e97d22cabef6d0404bff05a436c15996b metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 4b5fce360bf0db096420ddf360cb05fb63abef9a metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 12c59130a589553031e8a732559d20225da263aa19d2b43b4f23f2ff47a13396 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: a0f2b7ecf70b39b1e7b84ddab845455bf81f04019ecf1810b9540809be18cfb5a5fcdeb90986c4b11d0d86c85d38ced387beb5248a97e75460019687346cca41 metadata/logs/engine.8601aa42-fe51-4525-9c37-cab125d4b9bf.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 7da08c3bcf057f5790aae85a316cc4c7e84e8dae metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 9822a8bb8f23ff4a5f546df0e1901dac8ce404c90cc9e864c932e858f342296c metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 20961f19fd0db8bf533ce8aa98d561c15d672364183fc007e488c01e40271698363b6d1e35edfd4d109b9863391b666e44cb49cbec572343804ee8aec795de28 metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha1.txt: 3a83e9297c5eca6e6de723837360f84464d4ee94 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha256.txt: 57f04fd3cbd44703b65a45ec0acd6b1e56243dd599476dff375f2c868198939d bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer/tagmanifest-sha512.txt: 7eca04aa9b2734f1b61e65c7f009cd6ddd45735a0c303dd0653b766f411e9fdea1255c5db384dd0b3f787f5b1920fbacdea475948ad439ac70e2589a09f42b46 bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/p48_5xer\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_implicit0/provenance')], 'duration': 0.0008646879996376811, 'start': 1685951465.802495, 'stop': 1685951465.803361, '$report_type': 'TestReport', 'item_index': 528, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_secondary_files_implicit - location: ('tests/test_provenance.py', 103, 'test_secondary_files_implicit') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - when: runtest - nodeid: tests/test_provenance.py::test_secondary_files_implicit - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_provenance.py::test_secondary_files_explicit - location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.003713201000209665, 'start': 1685951465.804359, 'stop': 1685951465.808074, '$report_type': 'TestReport', 'item_index': 642, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_tmpdir.py::test_leave_tmpdirs', 'location': ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs'), 'keywords': {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env4.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env4.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env4.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env4.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env4.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python3"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "env0.py"\n }\n]\nDEBUG cwltool:job.py:215 [job env4.cwl] initial work dir {\n "_:71d3e5f1-6a63-4f12-8e4e-da560d54b9f0": [\n "import os\\nfor k, v in os.environ.items():\\n print(f\\"{k}={v}\\", end=\\"\\\\0\\")\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/env0.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job env4.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj$ python3 \\\n env0.py > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env4.cwl] completed success\nDEBUG cwltool:job.py:422 [job env4.cwl] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b",\n "basename": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameroot": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6da6366e8e172fcac257989bcfedf15da64e9a2a",\n "size": 1261,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/out/062565172eb482b02386f50adec0303a9a80c77b\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.8227042449998407, 'start': 1685951464.986022, 'stop': 1685951465.8087091, '$report_type': 'TestReport', 'item_index': 637, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_tmpdir.py::test_leave_tmpdirs', 'location': ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs'), 'keywords': {'test_leave_tmpdirs': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/env4.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/env4.cwl"\n}\nDEBUG cwltool:command_line_tool.py:982 [job env4.cwl] initializing from file:///Users/jasperk/gitlab/cwltool/tests/env4.cwl\nDEBUG cwltool:command_line_tool.py:988 [job env4.cwl] {}\nDEBUG cwltool:command_line_tool.py:1000 [job env4.cwl] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job env4.cwl] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "python3"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "env0.py"\n }\n]\nDEBUG cwltool:job.py:215 [job env4.cwl] initial work dir {\n "_:71d3e5f1-6a63-4f12-8e4e-da560d54b9f0": [\n "import os\\nfor k, v in os.environ.items():\\n print(f\\"{k}={v}\\", end=\\"\\\\0\\")\\n",\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/env0.py",\n "CreateFile",\n true\n ]\n}\nINFO cwltool:job.py:266 [job env4.cwl] /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj$ python3 \\\n env0.py > /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job env4.cwl] completed success\nDEBUG cwltool:job.py:422 [job env4.cwl] outputs {\n "env": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b",\n "basename": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameroot": "062565172eb482b02386f50adec0303a9a80c77b",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$6da6366e8e172fcac257989bcfedf15da64e9a2a",\n "size": 1261,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:process.py:347 Moving /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/tmp/xq6alzgj/062565172eb482b02386f50adec0303a9a80c77b to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_leave_tmpdirs0/out/062565172eb482b02386f50adec0303a9a80c77b\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.019946255999457208, 'start': 1685951465.809982, 'stop': 1685951465.82993, '$report_type': 'TestReport', 'item_index': 637, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_explicit', 'location': ('tests/test_provenance.py', 119, 'test_secondary_files_explicit'), 'keywords': {'test_secondary_files_explicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.022172081999997317, 'start': 1685951465.808274, 'stop': 1685951465.8304498, '$report_type': 'TestReport', 'item_index': 529, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_tmpdir.py::test_leave_tmpdirs - location: ('tests/test_tmpdir.py', 278, 'test_leave_tmpdirs') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0019066180002482724, 'start': 1685951465.833351, 'stop': 1685951465.835259, '$report_type': 'TestReport', 'item_index': 640, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_target.py::test_wrong_target', 'location': ('tests/test_target.py', 12, 'test_wrong_target'), 'keywords': {'test_wrong_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mI'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\nERROR cwltool:main.py:1218 I'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'")], 'duration': 1.5277158919998328, 'start': 1685951464.511601, 'stop': 1685951466.0392802, '$report_type': 'TestReport', 'item_index': 628, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_target.py::test_wrong_target', 'location': ('tests/test_target.py', 12, 'test_wrong_target'), 'keywords': {'test_wrong_target': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\n\x1b[1;30mERROR\x1b[0m \x1b[31mI'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'\x1b[0m\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl'\nERROR cwltool:main.py:1218 I'm sorry, I couldn't load this CWL file, try again with --debug for more information.\nThe error was: 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.cwl#main/dummy_target'")], 'duration': 0.00023238100038724951, 'start': 1685951466.039777, 'stop': 1685951466.040011, '$report_type': 'TestReport', 'item_index': 628, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_target.py::test_wrong_target - location: ('tests/test_target.py', 12, 'test_wrong_target') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]'), 'keywords': {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0021708399999624817, 'start': 1685951466.04311, 'stop': 1685951466.0452821, '$report_type': 'TestReport', 'item_index': 638, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_target.py::test_target_packed', 'location': ('tests/test_target.py', 29, 'test_target_packed'), 'keywords': {'test_target_packed': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#echo as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmp4ub_5xg8\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpqn2zozpb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxsls6qw3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplfi3vkzu\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.532981734000714, 'start': 1685951464.525578, 'stop': 1685951466.0585248, '$report_type': 'TestReport', 'item_index': 629, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_target.py::test_target_packed', 'location': ('tests/test_target.py', 29, 'test_target_packed'), 'keywords': {'test_target_packed': 1, 'test_target.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "out": [\n "foo INP1 INP2"\n ]\n}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json'\n\x1b[1;30mINFO\x1b[0m [workflow _15] start\n\x1b[1;30mINFO\x1b[0m [workflow _15] starting step step1_2\n\x1b[1;30mINFO\x1b[0m [step step1_2] start\n\x1b[1;30mINFO\x1b[0m [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\n\x1b[1;30mINFO\x1b[0m [job step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_2] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _15] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json",\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _15] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main\nINFO cwltool:workflow_job.py:765 [workflow _15] start\nDEBUG cwltool:workflow_job.py:777 [workflow _15] inputs {\n "inp1": [\n "INP1"\n ],\n "inp2": [\n "INP2"\n ]\n}\nINFO cwltool:workflow_job.py:613 [workflow _15] starting step step1_2\nINFO cwltool:workflow_job.py:75 [step step1_2] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#echo as part of step step1_2\nDEBUG cwltool:command_line_tool.py:988 [job step1_2] {\n "echo_in1": "INP1",\n "echo_in2": "INP2"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "echo"\n },\n {\n "position": [\n 0,\n 0\n ],\n "datum": "-n"\n },\n {\n "position": [\n 0,\n 1\n ],\n "datum": "foo"\n },\n {\n "position": [\n 0,\n "echo_in1"\n ],\n "datum": "INP1"\n },\n {\n "position": [\n 0,\n "echo_in2"\n ],\n "datum": "INP2"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_2] initial work dir {}\nINFO cwltool:job.py:266 [job step1_2] /private/tmp/docker_tmpxsls6qw3$ echo \\\n -n \\\n foo \\\n INP1 \\\n INP2 > /private/tmp/docker_tmpxsls6qw3/step1_out\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_2] completed success\nDEBUG cwltool:job.py:422 [job step1_2] outputs {\n "echo_out": "foo INP1 INP2"\n}\nDEBUG cwltool:workflow_job.py:564 [step step1_2] produced output {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/scatter-wf4.json#main/step1/echo_out": [\n "foo INP1 INP2"\n ]\n}\nINFO cwltool:workflow_job.py:572 [step step1_2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _15] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _15] outputs {\n "out": [\n "foo INP1 INP2"\n ]\n}\nDEBUG cwltool:job.py:446 [job step1_2] Removing input staging directory /private/tmp/docker_tmp4ub_5xg8\nDEBUG cwltool:job.py:454 [job step1_2] Removing temporary directory /private/tmp/docker_tmpqn2zozpb\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpxsls6qw3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmplfi3vkzu\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0004789479999089963, 'start': 1685951466.0598578, 'stop': 1685951466.060338, '$report_type': 'TestReport', 'item_index': 629, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_target.py::test_target_packed - location: ('tests/test_target.py', 29, 'test_target_packed') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]'), 'keywords': {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.002468566999596078, 'start': 1685951466.062423, 'stop': 1685951466.064893, '$report_type': 'TestReport', 'item_index': 639, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script\n [-h] --foo.one FOO.ONE --foo.two FOO.TWO [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --foo.one FOO.ONE\n --foo.two FOO.TWO\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'")], 'duration': 0.6442673579995244, 'start': 1685951465.835901, 'stop': 1685951466.480154, '$report_type': 'TestReport', 'item_index': 640, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script\n [-h] --foo.one FOO.ONE --foo.two FOO.TWO [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --foo.one FOO.ONE\n --foo.two FOO.TWO\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw4/test_argparse_help_with_c__n__0/script'")], 'duration': 0.00038592599958064966, 'start': 1685951466.4809642, 'stop': 1685951466.481351, '$report_type': 'TestReport', 'item_index': 640, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help with c-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n type: record\n fields:\n one: File\n two: string\n\nexpression: $(inputs.foo.two)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help with c-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n type: record\\n fields:\\n one: File\\n two: string\\n\\nexpression: $(inputs.foo.two)\\n\\noutputs: []\\n-]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparser_with_doc - location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_with_doc', 'location': ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc'), 'keywords': {'test_argparser_with_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002025419998972211, 'start': 1685951466.483218, 'stop': 1685951466.4834208, '$report_type': 'TestReport', 'item_index': 645, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_with_doc', 'location': ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc'), 'keywords': {'test_argparser_with_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'")], 'duration': 0.011666497999613057, 'start': 1685951466.483816, 'stop': 1685951466.4954839, '$report_type': 'TestReport', 'item_index': 645, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_with_doc', 'location': ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc'), 'keywords': {'test_argparser_with_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/with_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/with_doc.cwl'")], 'duration': 0.0002207099996667239, 'start': 1685951466.496104, 'stop': 1685951466.496326, '$report_type': 'TestReport', 'item_index': 645, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparser_with_doc - location: ('tests/test_toolargparse.py', 181, 'test_argparser_with_doc') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse_append_with_default[job_order1-expected_values1]', 'location': ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order1-expected_values1]'), 'keywords': {'test_argparse_append_with_default[job_order1-expected_values1]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order1-expected_values1': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005410029998529353, 'start': 1685951466.498595, 'stop': 1685951466.499137, '$report_type': 'TestReport', 'item_index': 648, 'worker_id': 'gw4', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '"cymbal2"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpqi4cps3i\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqi4cps3i\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.714671594999345, 'start': 1685951465.808789, 'stop': 1685951466.523444, '$report_type': 'TestReport', 'item_index': 642, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '"cymbal2"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpqi4cps3i\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_d__n___0/script",\n "foo": "cymbal2"\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpqi4cps3i\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.000832688000627968, 'start': 1685951466.5242019, 'stop': 1685951466.525036, '$report_type': 'TestReport', 'item_index': 642, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with d-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo:\n type:\n - type: enum\n symbols: [cymbal1, cymbal2]\n\nexpression: $(inputs.foo)\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with d-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo:\\n type:\\n - type: enum\\n symbols: [cymbal1, cymbal2]\\n\\nexpression: $(inputs.foo)\\n\\noutputs: []\\n-]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0017929050000020652, 'start': 1685951466.527004, 'stop': 1685951466.5287979, '$report_type': 'TestReport', 'item_index': 643, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]'), 'keywords': {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjo7d5ug0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_9] initial work dir {}\nINFO cwltool:job.py:266 [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_9] completed success\nDEBUG cwltool:job.py:422 [job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\nDEBUG cwltool:job.py:454 [job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjo7d5ug0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.6606748949998291, 'start': 1685951466.046178, 'stop': 1685951466.70684, '$report_type': 'TestReport', 'item_index': 638, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]'), 'keywords': {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script\n [-h] --bdg [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --bdg\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'")], 'duration': 0.6429743959997722, 'start': 1685951466.065346, 'stop': 1685951466.7083058, '$report_type': 'TestReport', 'item_index': 639, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]'), 'keywords': {'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{\n "output": {\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt",\n "basename": "test.txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "path": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt"\n }\n}'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] initial work dir {}\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mCould not collect memory usage, job ended before monitoring began.\x1b[0m\n\x1b[1;30mINFO\x1b[0m [job script_9] completed success\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32m[job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mMoving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjo7d5ug0\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script",\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:982 [job script_9] initializing from file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/script\nDEBUG cwltool:command_line_tool.py:988 [job script_9] {\n "input": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job script_9] path mappings is {\n "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl": [\n "/Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job script_9] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "cat"\n },\n {\n "position": [\n 0,\n "input"\n ],\n "datum": {\n "class": "File",\n "location": "file:///Users/jasperk/gitlab/cwltool/tests/echo.cwl",\n "size": 297,\n "basename": "echo.cwl",\n "nameroot": "echo",\n "nameext": ".cwl",\n "path": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl",\n "dirname": "/private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7"\n }\n }\n]\nDEBUG cwltool:job.py:215 [job script_9] initial work dir {}\nINFO cwltool:job.py:266 [job script_9] /private/tmp/docker_tmpjo7d5ug0$ cat \\\n /private/tmp/docker_tmpxf_4m4tq/stg1c16bae8-dbd0-40af-8209-4d8898c902b7/echo.cwl > /private/tmp/docker_tmpjo7d5ug0/test.txt\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job script_9] completed success\nDEBUG cwltool:job.py:422 [job script_9] outputs {\n "output": {\n "location": "file:///private/tmp/docker_tmpjo7d5ug0/test.txt",\n "basename": "test.txt",\n "nameroot": "test",\n "nameext": ".txt",\n "class": "File",\n "checksum": "sha1$51ab9f6e1e82d51d9ceefe816073058fe9f381ec",\n "size": 297,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:job.py:446 [job script_9] Removing input staging directory /private/tmp/docker_tmpxf_4m4tq\nDEBUG cwltool:job.py:454 [job script_9] Removing temporary directory /private/tmp/docker_tmp3zh1i2gg\nDEBUG cwltool:process.py:347 Moving /private/tmp/docker_tmpjo7d5ug0/test.txt to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw2/test_argparse_help__n___usr_bi0/outdir/test.txt\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjo7d5ug0\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0010807290000229841, 'start': 1685951466.7084632, 'stop': 1685951466.709545, '$report_type': 'TestReport', 'item_index': 638, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]'), 'keywords': {'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', 'usage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script\n [-h] --bdg [job_order]\n\npositional arguments:\n job_order Job input json file\n\noptions:\n -h, --help show this help message and exit\n --bdg\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script' to 'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw7/test_argparse_boolean__n___usr0/script'")], 'duration': 0.00043712600017897785, 'start': 1685951466.709005, 'stop': 1685951466.709443, '$report_type': 'TestReport', 'item_index': 639, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='teardown' outcome='passed'> [hook] - finish pytest_report_from_serializable --> ]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse[boolean-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ninputs:\n - id: bdg\n type: "boolean"\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: foo\nbaseCommand:\n - echo\n - "ff"\nstdout: foo\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[boolean-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ninputs:\\n - id: bdg\\n type: "boolean"\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: foo\\nbaseCommand:\\n - echo\\n - "ff"\\nstdout: foo\\n-]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logreport [hook] - report: ]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse[help-\n#!/usr/bin/env cwl-runner\ncwlVersion: v1.0\nclass: CommandLineTool\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\ninputs:\n #Give it a list of input files\n - id: input\n type: File\n inputBinding:\n position: 0\noutputs:\n - id: output\n type: File\n outputBinding:\n glob: test.txt\nstdout: test.txt\nbaseCommand: [cat]\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[help-\\n#!/usr/bin/env cwl-runner\\ncwlVersion: v1.0\\nclass: CommandLineTool\\ndoc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"\\ninputs:\\n #Give it a list of input files\\n - id: input\\n type: File\\n inputBinding:\\n position: 0\\noutputs:\\n - id: output\\n type: File\\n outputBinding:\\n glob: test.txt\\nstdout: test.txt\\nbaseCommand: [cat]\\n-]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0] - location: ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_argparser_without_doc - location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse_append_with_default[job_order0-expected_values0]', 'location': ('tests/test_toolargparse.py', 199, 'test_argparse_append_with_default[job_order0-expected_values0]'), 'keywords': {'test_argparse_append_with_default[job_order0-expected_values0]': 1, 'parametrize': 1, 'pytestmark': 1, 'job_order0-expected_values0': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005423120001069037, 'start': 1685951466.713546, 'stop': 1685951466.7140899, '$report_type': 'TestReport', 'item_index': 647, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_without_doc', 'location': ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc'), 'keywords': {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00038347800000337884, 'start': 1685951466.7141151, 'stop': 1685951466.7145011, '$report_type': 'TestReport', 'item_index': 646, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_without_doc', 'location': ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc'), 'keywords': {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'")], 'duration': 0.019146607000038784, 'start': 1685951466.715123, 'stop': 1685951466.734271, '$report_type': 'TestReport', 'item_index': 646, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparser_without_doc', 'location': ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc'), 'keywords': {'test_argparser_without_doc': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:06]\x1b[0m \x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'\n"), ('Captured log call', "INFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/without_doc.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/without_doc.cwl'")], 'duration': 0.00028543000007630326, 'start': 1685951466.734833, 'stop': 1685951466.7351198, '$report_type': 'TestReport', 'item_index': 646, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparser_without_doc - location: ('tests/test_toolargparse.py', 190, 'test_argparser_without_doc') - 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/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ab5d55af482cae1b1829c3da3ee604ee1fb46e6c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: e16b2b9f3a4ea3c4db3ad2bb71e39cdd02c1fde2a446528a68596c88de6ce0ad workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0173fb349bad74105b30c7b54ebfc79bc650689ee08d2810530ae536a1b064eaf25c7b9f15d9c9dfd3e685437e64a2e8d5c55dd9ac21dae1ac0ee2dc95b3c641 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmp9gj9l2fa\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp46c_retm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5ft4gx95\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp96w7gil\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 509e405f0bd8ef93211df57e39be176d12666adc metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 262ec7432d66db0b5ed1cd59aa1af4cd4be1124dbc4af94e86bb6b512289b670 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0119a8de57eb87221919bb6f241bdbe06282b70055adb1d5ae33b9c6f69d081928b3f227305cef219b208ab543d013f5244e55ec7b86517988eaed08f44786f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 45b1c340c57cf230ed17b4e630abdf1efade240e metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: eb6898093916925d311c393e4d05c7526bb1cc611d0dde25b34dd9e93b53bbc4 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 3bf0f3cd885ac1a11daa3a4ddd0c2a1629c6ca2c4ebbb55721070a7aab577a15e431939a7983d567fdfc52b7c6cd4ac9cc7301dc550254a3f5c54bc614f33337 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 38e4d26d88163d39f1f79746d91c385a30ee9225 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0541fdfe699859ca640f637778cffea97fd5bb4b10fae765cca532bb51594598 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: dd848f7099d65e87f01861744621b13563715b0af772ac3f9c254aaf22da244075483bb03cd153771798371887f6435b579e557f5fc8e0b55abcbd63d11b3671 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0a9161af759436c0940176a0ee92ac46d033a8d2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d975c4b3006cb518b3712877f983b68a2f38e2860b23bbda21d4d5c6bc82482d metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: af800227b8ede5af124ae87add535d60d7565a31b2e0923532a6442d21e755820ef1dee20d54db2aae2585bbdc1f1d566b1a76a4d251b80d6183146da3b14b9c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 6f16628a75ecb5bc263b08aa80b2b04c289f6b85 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d7a309d015efc43f7c0d10319bd7866a9e569b1ceb945c129bfc0108f1baeeb7 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 60585141255cb9b43faafbfa26e49d21ddaeff3718becc211fc229d7b9dc2201ae89245239fc3ff9e03726bd8d99faa864df8eb661810117fb2a43f868188cb3 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0077decebf928c4d8aebf6cd1b9c40ae95443eb6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ccfe9486f117718bb534393411f3535d23abe939688867cd7fb7666948a96040 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 5f7ed9ffdc499c78afe431fa0d3ed7bd2942590ddb4cdb42b728daae7644af1f50f352669a364b61880354e56de96674c7b9faa918f33ebd112dc80f3194aa5a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ecdb0d529e82bcfae2510df67a6c624ec91cb4eb metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: f3498f65cdd7f44b2f46cdc5f8a6630bd922452b6bed63648fd8a0b0636b53e9 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 140511736f43c0e44321a2d677bb2e54684fa8e564d650558381799123517ea7a27402ecf6c826c0651360dbc351f4903847f1dc7552ecbc7bc5f372963395f7 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b73fda4904dd1bea80c96c9fc89e49aabbd83fff metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 9f14d52b82857ac1b7a45eb1bf0f6ee22105533f54c1af788fec3744102e8d97 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: b5c96592dbe7dd23e27053f734d227f91c089e42395a9a812dc4994fce5850b58c7ae04d804f92a0041ed0487a26a4e0011cd626bcd86621ae9cd773d631daae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: a28a0bc657b6e1797cdbfe4343a9adfad7fbc539 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: b32be96d6dc9f72b299be94d867dd45f884d5e0f5c416b98f8f03e691ddecec3 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 6145e7ae857af5949152de4f2773425ea722b736616597d7c4766ad6b85b57435c37240b545b770e500e565af57ba9ae25b498dfaa8c31003b65f066cfb9a62b bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance')], 'duration': 1.0753109860006589, 'start': 1685951465.8310468, 'stop': 1685951466.9063349, '$report_type': 'TestReport', 'item_index': 529, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_provenance.py::test_secondary_files_explicit', 'location': ('tests/test_provenance.py', 119, 'test_secondary_files_explicit'), 'keywords': {'test_secondary_files_explicit': 1, 'skipif': 1, 'pytestmark': 1, 'test_provenance.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '{}'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl'\n\x1b[1;30mINFO\x1b[0m Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\n\x1b[1;30mINFO\x1b[0m [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\n\x1b[1;30mINFO\x1b[0m [workflow _20] start\n\x1b[1;30mINFO\x1b[0m [workflow _20] starting step step1_4\n\x1b[1;30mINFO\x1b[0m [step step1_4] start\n\x1b[1;30mINFO\x1b[0m [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\n\x1b[1;30mINFO\x1b[0m [job step1_3] completed success\n\x1b[1;30mINFO\x1b[0m [step step1_4] completed success\n\x1b[1;30mINFO\x1b[0m [workflow _20] completed success\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m [provenance] Finalizing Research Object\n\x1b[1;30mINFO\x1b[0m [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n\x1b[1;30mINFO\x1b[0m [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\n"), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:ro.py:95 [provenance] Temporary research object: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nDEBUG cwltool:writablebagfile.py:136 [provenance] Opening log file for engine: metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt.\nDEBUG cwltool:main.py:705 [provenance] Logging to <_io.TextIOWrapper name=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\' encoding=\'UTF-8\'>\nINFO cwltool:main.py:708 [cwltool] --provenance /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance /Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\nDEBUG cwltool:main.py:709 [cwltool] Arguments: Namespace(basedir=None, outdir=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/cwltool-run\', log_dir=\'\', parallel=False, preserve_environment=[], preserve_entire_environment=False, rm_container=True, record_container_id=False, cidfile_dir=None, cidfile_prefix=None, tmpdir_prefix=\'/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/\', tmp_outdir_prefix=\'\', cachedir=\'\', rm_tmpdir=True, move_outputs=\'move\', pull_image=True, rdf_serializer=\'turtle\', eval_timeout=60, provenance=\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\', user_provenance=False, host_provenance=False, orcid=\'\', cwl_full_name=\'\', no_data=False, print_rdf=False, print_dot=False, print_pre=False, print_deps=False, print_input_deps=False, pack=False, version=False, validate=False, print_supported_versions=False, print_subgraph=False, print_targets=False, make_template=False, strict=True, skip_schemas=False, doc_cache=True, verbose=False, quiet=False, debug=False, write_summary=\'\', strict_memory_limit=False, strict_cpu_limit=False, timestamps=False, js_console=False, disable_js_validation=False, js_hint_options_file=None, user_space_docker_cmd=None, singularity=False, podman=False, use_container=True, beta_dependency_resolvers_configuration=None, beta_dependencies_directory=None, beta_use_biocontainers=None, beta_conda_dependencies=None, tool_help=False, relative_deps=\'primary\', enable_dev=False, enable_ext=False, enable_color=True, default_container=None, no_match_user=False, custom_net=None, do_validate=True, fast_parser=False, enable_ga4gh_tool_registry=True, ga4gh_tool_registries=[], on_error=\'stop\', compute_checksum=True, relax_path_checks=False, force_docker_pull=False, no_read_only=False, overrides=None, target=None, single_step=None, single_process=None, mpi_config_file=None, workflow=\'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\', job_order=[\'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/job.json\'])\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\'\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/packed.cwl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 15105a71be9e70c7817e948ad77f33f11d85793b workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0eca35d960955ad46d824e494b8c1a8781b94d9593e1dd681301d14e81b0392e workflow/packed.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 053b5a51ac96e2c2e13056d7a1a2bf31017af0a895014fbd7f158a90eddf36a6fa61c81c73c921997604367b07bd6b3a37bf48c93caad649e2dc9a7b86bd2540 workflow/packed.cwl\n\nDEBUG cwltool:writablebagfile.py:237 [provenance] Added packed workflow: workflow/packed.cwl\nINFO cwltool:main.py:1153 Writing workflow rdf to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmp_ujdgzqd/workflow.ttl\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'file1\': {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}}\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt\', \'secondaryFiles\': [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}], \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\', \'size\': 3, \'nameroot\': \'foo1\', \'nameext\': \'.txt\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: [{\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {\'class\': \'File\', \'basename\': \'foo1.txt.idx\', \'location\': \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\', \'size\': 3, \'nameroot\': \'foo1.txt\', \'nameext\': \'.idx\'}\nINFO cwltool:ro.py:610 [provenance] Adding to RO file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/manifest-sha1.txt: 62cdb7020ff920e5aa642c3d4066950dd1f01f4d data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\n\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: File\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt.idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1.txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .idx\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:591 [provenance] Relativising: ../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:591 [provenance] Relativising: 3\nDEBUG cwltool:ro.py:591 [provenance] Relativising: foo1\nDEBUG cwltool:ro.py:591 [provenance] Relativising: .txt\nDEBUG cwltool:ro.py:591 [provenance] Relativising: sha1$0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-job.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ab5d55af482cae1b1829c3da3ee604ee1fb46e6c workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: e16b2b9f3a4ea3c4db3ad2bb71e39cdd02c1fde2a446528a68596c88de6ce0ad workflow/primary-job.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0173fb349bad74105b30c7b54ebfc79bc650689ee08d2810530ae536a1b064eaf25c7b9f15d9c9dfd3e685437e64a2e8d5c55dd9ac21dae1ac0ee2dc95b3c641 workflow/primary-job.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-job.json\nDEBUG cwltool:workflow_job.py:498 [workflow _20] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nINFO cwltool:workflow_job.py:765 [workflow _20] start\nDEBUG cwltool:workflow_job.py:777 [workflow _20] inputs {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:613 [workflow _20] starting step step1_4\nDEBUG cwltool:workflow_job.py:727 [step step1_4] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:workflow_job.py:732 [step step1_4] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-wf.cwl#step1/file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nINFO cwltool:workflow_job.py:75 [step step1_4] start\nDEBUG cwltool:command_line_tool.py:982 [job step1_3] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/sec-tool.cwl as part of step step1_4\nDEBUG cwltool:command_line_tool.py:988 [job step1_3] {\n "file1": {\n "class": "File",\n "basename": "foo1.txt",\n "secondaryFiles": [\n {\n "class": "File",\n "basename": "foo1.txt.idx",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "size": 3,\n "nameroot": "foo1.txt",\n "nameext": ".idx"\n }\n ],\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "size": 3,\n "nameroot": "foo1",\n "nameext": ".txt"\n }\n}\nDEBUG cwltool:command_line_tool.py:1000 [job step1_3] path mappings is {\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/foo/foo",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt",\n "File",\n true\n ],\n "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar": [\n "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/bar/bar",\n "/private/tmp/docker_tmp9gj9l2fa/stgd0b7e2c0-850a-4cdc-ac83-84a15b5a0d85/foo1.txt.idx",\n "File",\n true\n ]\n}\nDEBUG cwltool:command_line_tool.py:1052 [job step1_3] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "true"\n }\n]\nDEBUG cwltool:job.py:215 [job step1_3] initial work dir {}\nINFO cwltool:job.py:266 [job step1_3] /private/tmp/docker_tmpp96w7gil$ true\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33\nDEBUG cwltool:ro.py:514 [provenance] Added data file /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:ro.py:520 [provenance] Relative path for data file data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d\nDEBUG cwltool:job.py:538 Could not collect memory usage, job ended before monitoring began.\nINFO cwltool:job.py:419 [job step1_3] completed success\nDEBUG cwltool:job.py:422 [job step1_3] outputs {}\nDEBUG cwltool:workflow_job.py:564 [step step1_4] produced output {}\nINFO cwltool:workflow_job.py:572 [step step1_4] completed success\nINFO cwltool:workflow_job.py:539 [workflow _20] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _20] outputs {}\nDEBUG cwltool:job.py:446 [job step1_3] Removing input staging directory /private/tmp/docker_tmp9gj9l2fa\nDEBUG cwltool:job.py:454 [job step1_3] Removing temporary directory /private/tmp/docker_tmp46c_retm\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp5ft4gx95\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpp96w7gil\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.xml.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 509e405f0bd8ef93211df57e39be176d12666adc metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 262ec7432d66db0b5ed1cd59aa1af4cd4be1124dbc4af94e86bb6b512289b670 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 0119a8de57eb87221919bb6f241bdbe06282b70055adb1d5ae33b9c6f69d081928b3f227305cef219b208ab543d013f5244e55ec7b86517988eaed08f44786f5 metadata/provenance/primary.cwlprov.xml\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.provn.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 45b1c340c57cf230ed17b4e630abdf1efade240e metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: eb6898093916925d311c393e4d05c7526bb1cc611d0dde25b34dd9e93b53bbc4 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 3bf0f3cd885ac1a11daa3a4ddd0c2a1629c6ca2c4ebbb55721070a7aab577a15e431939a7983d567fdfc52b7c6cd4ac9cc7301dc550254a3f5c54bc614f33337 metadata/provenance/primary.cwlprov.provn\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 38e4d26d88163d39f1f79746d91c385a30ee9225 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 0541fdfe699859ca640f637778cffea97fd5bb4b10fae765cca532bb51594598 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: dd848f7099d65e87f01861744621b13563715b0af772ac3f9c254aaf22da244075483bb03cd153771798371887f6435b579e557f5fc8e0b55abcbd63d11b3671 metadata/provenance/primary.cwlprov.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.ttl.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0a9161af759436c0940176a0ee92ac46d033a8d2 metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d975c4b3006cb518b3712877f983b68a2f38e2860b23bbda21d4d5c6bc82482d metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: af800227b8ede5af124ae87add535d60d7565a31b2e0923532a6442d21e755820ef1dee20d54db2aae2585bbdc1f1d566b1a76a4d251b80d6183146da3b14b9c metadata/provenance/primary.cwlprov.ttl\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.nt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 6f16628a75ecb5bc263b08aa80b2b04c289f6b85 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: d7a309d015efc43f7c0d10319bd7866a9e569b1ceb945c129bfc0108f1baeeb7 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 60585141255cb9b43faafbfa26e49d21ddaeff3718becc211fc229d7b9dc2201ae89245239fc3ff9e03726bd8d99faa864df8eb661810117fb2a43f868188cb3 metadata/provenance/primary.cwlprov.nt\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/provenance/primary.cwlprov.jsonld.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 0077decebf928c4d8aebf6cd1b9c40ae95443eb6 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ccfe9486f117718bb534393411f3535d23abe939688867cd7fb7666948a96040 metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 5f7ed9ffdc499c78afe431fa0d3ed7bd2942590ddb4cdb42b728daae7644af1f50f352669a364b61880354e56de96674c7b9faa918f33ebd112dc80f3194aa5a metadata/provenance/primary.cwlprov.jsonld\n\nDEBUG cwltool:provenance_profile.py:777 [provenance] added provenance: [, , , , , ]\nDEBUG cwltool:ro.py:591 [provenance] Relativising: {}\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/workflow/primary-output.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 5f36b2ea290645ee34d943220a14b54ee5ea5be5 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: ca3d163bab055381827226140568f3bef7eaac187cebd76878e0b63e9e442356 workflow/primary-output.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: ca4b6defb8adcc010050bc8b1bb8f8092c4928b8a0fba32146abcfb256e4d91672f88ca2cdf6210e754e5b8ac5e23fb023806ccd749ac8b701f79a691f03c87a workflow/primary-output.json\n\nDEBUG cwltool:writablebagfile.py:259 [provenance] Generated customised job file: workflow/primary-output.json\nINFO cwltool:main.py:1366 Final process status is success\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: 3825ba9b0a5e9fcfd6668aa473442a99faba6612 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: cd0cc685d2e80738b9bf1fe039c667dc35d30ecd8761acd523846268dd35a879 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 640a50f563afa32de58fa7ab601b250113a45cb845f09feb21f3975da3396e07095cf2ce00e70d12e087a6b9202975fff695847f45f0bd99a76f4bf5a5de8851 snapshot/sec-wf.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b26ea4d046f1bddce51ead23fe9841f4eab634c2 snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 6ef6b48300501ce4e2b582bbeb458a2b0287cbd47d8b762c12a16c5c2034461d snapshot/sec-tool.cwl\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 12ca6134766900b6e73dd3d4ba2deda5e48801672436e9e397e3906976548ee61707e2d0c3ca041792cac5273a167bfb1b05b9278cd0ec3d4f86a7a20d7e88cd snapshot/sec-tool.cwl\n\nDEBUG cwltool:main.py:1416 [provenance] Closing provenance log file \nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: ecdb0d529e82bcfae2510df67a6c624ec91cb4eb metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: f3498f65cdd7f44b2f46cdc5f8a6630bd922452b6bed63648fd8a0b0636b53e9 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 140511736f43c0e44321a2d677bb2e54684fa8e564d650558381799123517ea7a27402ecf6c826c0651360dbc351f4903847f1dc7552ecbc7bc5f372963395f7 metadata/logs/engine.09cc43c0-e65b-4f82-af38-24dcbaff623f.txt\n\nINFO cwltool:writablebagfile.py:217 [provenance] Finalizing Research Object\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/metadata/manifest.json.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: b73fda4904dd1bea80c96c9fc89e49aabbd83fff metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: 9f14d52b82857ac1b7a45eb1bf0f6ee22105533f54c1af788fec3744102e8d97 metadata/manifest.json\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: b5c96592dbe7dd23e27053f734d227f91c089e42395a9a812dc4994fce5850b58c7ae04d804f92a0041ed0487a26a4e0011cd626bcd86621ae9cd773d631daae metadata/manifest.json\n\nDEBUG cwltool:writablebagfile.py:52 [provenance] Creating WritableBagFile at /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/bag-info.txt.\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha1.txt: a28a0bc657b6e1797cdbfe4343a9adfad7fbc539 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha256.txt: b32be96d6dc9f72b299be94d867dd45f884d5e0f5c416b98f8f03e691ddecec3 bag-info.txt\n\nDEBUG cwltool:ro.py:558 [provenance] Added to /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i/tagmanifest-sha512.txt: 6145e7ae857af5949152de4f2773425ea722b736616597d7c4766ad6b85b57435c37240b545b770e500e565af57ba9ae25b498dfaa8c31003b65f066cfb9a62b bag-info.txt\n\nDEBUG cwltool:writablebagfile.py:188 [provenance] Generated bagit metadata: /var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/48ox934i\nINFO cwltool:writablebagfile.py:222 [provenance] Deleting existing /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance\nINFO cwltool:writablebagfile.py:225 [provenance] Research Object saved to /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_secondary_files_explicit0/provenance')], 'duration': 0.0012781379991793074, 'start': 1685951466.908513, 'stop': 1685951466.9097931, '$report_type': 'TestReport', 'item_index': 529, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_provenance.py::test_secondary_files_explicit - location: ('tests/test_provenance.py', 119, 'test_secondary_files_explicit') - finish pytest_runtest_logfinish --> [] [hook] - pytest_warning_recorded [hook] - warning_message: {message : UserWarning('NTSerializer always uses UTF-8 encoding. Given encoding was: None'), category : 'UserWarning', filename : '/Users/jasperk/gitlab/cwltool/venv/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py', lineno : 40, line : None} - when: runtest - nodeid: tests/test_provenance.py::test_secondary_files_explicit - location: None - finish pytest_warning_recorded --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_toolargparse.py::test_dont_require_inputs - location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_dont_require_inputs', 'location': ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs'), 'keywords': {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0014646170002379222, 'start': 1685951466.91312, 'stop': 1685951466.914585, '$report_type': 'TestReport', 'item_index': 644, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '"{\\"bar\\": http://example.com}"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjyzejhiw\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjyzejhiw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.7014808530002483, 'start': 1685951466.5291898, 'stop': 1685951467.230655, '$report_type': 'TestReport', 'item_index': 643, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]', 'location': ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]'), 'keywords': {'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]': 1, 'parametrize': 1, 'skipif': 1, 'pytestmark': 1, 'foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '"{\\"bar\\": http://example.com}"'), ('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mRemoving intermediate output directory /private/tmp/docker_tmpjyzejhiw\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw6/test_argparse_foo_with_e__n___0/script",\n "foo": {\n "class": "File",\n "location": "http://example.com"\n }\n}\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpjyzejhiw\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.0005410029998529353, 'start': 1685951467.23134, 'stop': 1685951467.231882, '$report_type': 'TestReport', 'item_index': 643, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> ]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: ]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: ]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_argparse[foo with e-\n#!/usr/bin/env cwl-runner\n\ncwlVersion: v1.0\nclass: ExpressionTool\n\ninputs:\n foo: File\n\nexpression: '{"bar": $(inputs.foo.location)}'\n\noutputs: []\n-] - location: ('tests/test_toolargparse.py', 125, 'test_argparse[foo with e-\\n#!/usr/bin/env cwl-runner\\n\\ncwlVersion: v1.0\\nclass: ExpressionTool\\n\\ninputs:\\n foo: File\\n\\nexpression: \'{"bar": $(inputs.foo.location)}\'\\n\\noutputs: []\\n-]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - 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Validating all objects:")], 'duration': 0.00020839900025748648, 'start': 1685951467.743108, 'stop': 1685951467.743317, '$report_type': 'TestReport', 'item_index': 655, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_validate.py::test_validate_graph_with_no_default - location: ('tests/test_validate.py', 6, 'test_validate_graph_with_no_default') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_validate_js.py::test_get_expressions - location: ('tests/test_validate_js.py', 24, 'test_get_expressions') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_validate_js.py::test_get_expressions', 'location': ('tests/test_validate_js.py', 24, 'test_get_expressions'), 'keywords': {'test_get_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.00021349599956010934, 'start': 1685951467.7448692, 'stop': 1685951467.7450838, '$report_type': 'TestReport', 'item_index': 656, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_with_step_level_default_value', 'location': ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value'), 'keywords': {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', 'latest: Pulling from library/alpine\nDigest: sha256:02bb6f428431fbc2809c5d1b41eab5a68350194fb508869a33cb1af4444c9b11\nStatus: Image is up to date for alpine:latest\ndocker.io/library/alpine:latest\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:argparser.py:943 Can\'t make command line argument from Any\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "message": "two"\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step task2\nDEBUG cwltool:workflow_job.py:727 [step task2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2] start\nDEBUG cwltool:command_line_tool.py:982 [job task2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2\nDEBUG cwltool:command_line_tool.py:988 [job task2] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/alpine:latest\']\nDEBUG cwltool:job.py:215 [job task2] initial work dir {}\nINFO cwltool:job.py:266 [job task2] /private/tmp/docker_tmp2vpjz9j3$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2vpjz9j3,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpbyyklcxx,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpwtgdio32/20230605095106-754192.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2] completed success\nDEBUG cwltool:job.py:422 [job task2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2vpjz9j3/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {}\nDEBUG cwltool:job.py:446 [job task2] Removing input staging directory /private/tmp/docker_tmpy2a25zaq\nDEBUG cwltool:job.py:454 [job task2] Removing temporary directory /private/tmp/docker_tmpbyyklcxx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2vpjz9j3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpysive81g\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 4.140258484999322, 'start': 1685951463.636079, 'stop': 1685951467.776237, '$report_type': 'TestReport', 'item_index': 623, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_subgraph.py::test_single_with_step_level_default_value', 'location': ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value'), 'keywords': {'test_single_with_step_level_default_value': 1, 'skipif': 1, 'pytestmark': 1, 'test_subgraph.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', 'latest: Pulling from library/alpine\nDigest: sha256:02bb6f428431fbc2809c5d1b41eab5a68350194fb508869a33cb1af4444c9b11\nStatus: Image is up to date for alpine:latest\ndocker.io/library/alpine:latest\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\' to \'file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\'\nDEBUG cwltool:argparser.py:943 Can\'t make command line argument from Any\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl"\n}\nDEBUG cwltool:workflow_job.py:498 [workflow _18] initialized from file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl\nINFO cwltool:workflow_job.py:765 [workflow _18] start\nDEBUG cwltool:workflow_job.py:777 [workflow _18] inputs {\n "message": "two"\n}\nINFO cwltool:workflow_job.py:613 [workflow _18] starting step task2\nDEBUG cwltool:workflow_job.py:727 [step task2] job input {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nDEBUG cwltool:workflow_job.py:732 [step task2] evaluated job input to {\n "file:///Users/jasperk/gitlab/cwltool/tests/wf/cache_test_workflow.cwl#task2/message": "two"\n}\nINFO cwltool:workflow_job.py:75 [step task2] start\nDEBUG cwltool:command_line_tool.py:982 [job task2] initializing from file:///Users/jasperk/gitlab/cwltool/tests/wf/touch_tool.cwl as part of step task2\nDEBUG cwltool:command_line_tool.py:988 [job task2] {\n "message": "two"\n}\nDEBUG cwltool:command_line_tool.py:1000 [job task2] path mappings is {}\nDEBUG cwltool:command_line_tool.py:1052 [job task2] command line bindings is [\n {\n "position": [\n -1000000,\n 0\n ],\n "datum": "touch"\n },\n {\n "position": [\n 1,\n "message"\n ],\n "datum": "two"\n }\n]\nINFO cwltool:docker.py:151 [\'docker\', \'pull\', \'docker.io/alpine:latest\']\nDEBUG cwltool:job.py:215 [job task2] initial work dir {}\nINFO cwltool:job.py:266 [job task2] /private/tmp/docker_tmp2vpjz9j3$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/private/tmp/docker_tmp2vpjz9j3,target=/KKDWnh \\\n --mount=type=bind,source=/private/tmp/docker_tmpbyyklcxx,target=/tmp \\\n --workdir=/KKDWnh \\\n --read-only=true \\\n --user=501:20 \\\n --rm \\\n --cidfile=/private/tmp/docker_tmpwtgdio32/20230605095106-754192.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/KKDWnh \\\n docker.io/alpine:latest \\\n touch \\\n two\nINFO cwltool:job.py:905 [job task2] Max memory used: 0MiB\nINFO cwltool:job.py:419 [job task2] completed success\nDEBUG cwltool:job.py:422 [job task2] outputs {\n "out": {\n "location": "file:///private/tmp/docker_tmp2vpjz9j3/two",\n "basename": "two",\n "nameroot": "two",\n "nameext": "",\n "class": "File",\n "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",\n "size": 0,\n "http://commonwl.org/cwltool#generation": 0\n }\n}\nDEBUG cwltool:workflow_job.py:564 [step task2] produced output {}\nINFO cwltool:workflow_job.py:572 [step task2] completed success\nINFO cwltool:workflow_job.py:539 [workflow _18] completed success\nDEBUG cwltool:workflow_job.py:541 [workflow _18] outputs {}\nDEBUG cwltool:job.py:446 [job task2] Removing input staging directory /private/tmp/docker_tmpy2a25zaq\nDEBUG cwltool:job.py:454 [job task2] Removing temporary directory /private/tmp/docker_tmpbyyklcxx\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmp2vpjz9j3\nDEBUG cwltool:process.py:398 Removing intermediate output directory /private/tmp/docker_tmpysive81g\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00046557099994970486, 'start': 1685951467.777664, 'stop': 1685951467.778131, '$report_type': 'TestReport', 'item_index': 623, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_subgraph.py::test_single_with_step_level_default_value - location: ('tests/test_subgraph.py', 287, 'test_single_with_step_level_default_value') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix - location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix'), 'keywords': {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.002130539000063436, 'start': 1685951467.780889, 'stop': 1685951467.783021, '$report_type': 'TestReport', 'item_index': 632, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix'), 'keywords': {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']\n"), ('Captured log call', "INFO cwltool:docker.py:164 ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']")], 'duration': 0.09524703099941689, 'start': 1685951467.7836092, 'stop': 1685951467.878856, '$report_type': 'TestReport', 'item_index': 632, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix', 'location': ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix'), 'keywords': {'test_dockerfile_tmpdir_prefix': 1, 'skipif': 1, 'pytestmark': 1, 'test_tmpdir.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:07]\x1b[0m \x1b[1;30mINFO\x1b[0m ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']\n"), ('Captured log call', "INFO cwltool:docker.py:164 ['docker', 'build', '--tag=test_dockerfile_tmpdir_prefix', '/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw3/test_dockerfile_tmpdir_prefix0/out/1m4fd70vd']")], 'duration': 0.003588997999941057, 'start': 1685951467.880084, 'stop': 1685951467.8836741, '$report_type': 'TestReport', 'item_index': 632, 'worker_id': 'gw3', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_tmpdir.py::test_dockerfile_tmpdir_prefix - location: ('tests/test_tmpdir.py', 111, 'test_dockerfile_tmpdir_prefix') - finish pytest_runtest_logfinish --> [] [hook] - pytest_testnodedown [hook] - node: - error: None - finish pytest_testnodedown --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_trs.py::test_tool_trs_template', 'location': ('tests/test_trs.py', 93, 'test_tool_trs_template'), 'keywords': {'test_tool_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\nINFO cwltool:load_tool.py:102 Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'")], 'duration': 0.6917008549999082, 'start': 1685951467.234879, 'stop': 1685951467.9265652, '$report_type': 'TestReport', 'item_index': 650, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_trs.py::test_tool_trs_template', 'location': ('tests/test_trs.py', 93, 'test_tool_trs_template'), 'keywords': {'test_tool_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/local/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4', '/usr/share/commonwl/quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl\nINFO cwltool:load_tool.py:102 Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl'")], 'duration': 0.00021415700030047446, 'start': 1685951467.9271948, 'stop': 1685951467.92741, '$report_type': 'TestReport', 'item_index': 650, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_trs.py::test_tool_trs_template - location: ('tests/test_trs.py', 93, 'test_tool_trs_template') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_validate_js.py::test_js_hint_basic - location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_basic', 'location': ('tests/test_validate_js.py', 53, 'test_js_hint_basic'), 'keywords': {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0002251839996461058, 'start': 1685951467.929321, 'stop': 1685951467.929547, '$report_type': 'TestReport', 'item_index': 658, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_basic', 'location': ('tests/test_validate_js.py', 53, 'test_js_hint_basic'), 'keywords': {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.010393084999122948, 'start': 1685951467.930013, 'stop': 1685951467.940408, '$report_type': 'TestReport', 'item_index': 658, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_validate_js.py::test_js_hint_basic', 'location': ('tests/test_validate_js.py', 53, 'test_js_hint_basic'), 'keywords': {'test_js_hint_basic': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0015349340001193923, 'start': 1685951467.940873, 'stop': 1685951467.942409, '$report_type': 'TestReport', 'item_index': 658, 'worker_id': 'gw6', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_validate_js.py::test_js_hint_basic - location: ('tests/test_validate_js.py', 53, 'test_js_hint_basic') - finish pytest_runtest_logfinish --> [] [hook] - pytest_testnodedown [hook] - node: - error: None - finish pytest_testnodedown --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_trs.py::test_workflow_trs_template', 'location': ('tests/test_trs.py', 107, 'test_workflow_trs_template'), 'keywords': {'test_workflow_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\nINFO cwltool:load_tool.py:102 Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'")], 'duration': 0.6574194070008161, 'start': 1685951467.625265, 'stop': 1685951468.282669, '$report_type': 'TestReport', 'item_index': 651, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_trs.py::test_workflow_trs_template', 'location': ('tests/test_trs.py', 107, 'test_workflow_trs_template'), 'keywords': {'test_workflow_trs_template': 1, '__wrapped__': 1, 'patchings': 1, 'test_trs.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', "input_file: # type 'File'\n class: File\n path: a/file/path\n"), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mSearch path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mHead path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mPassed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\x1b[0m\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mResolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\x1b[0m\n\x1b[1;30mINFO\x1b[0m Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nDEBUG cwltool:resolver.py:33 Search path is ['/Users/jasperk/.local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/local/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop', '/usr/share/commonwl/#workflow/github.com/dockstore-testing/md5sum-checker:develop']\nDEBUG cwltool:resolver.py:74 Head path is https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:78 Passed head path of https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files\nDEBUG cwltool:resolver.py:90 Resolved https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl\nINFO cwltool:load_tool.py:102 Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl'")], 'duration': 0.0025651939995441353, 'start': 1685951468.283201, 'stop': 1685951468.285768, '$report_type': 'TestReport', 'item_index': 651, 'worker_id': 'gw7', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_trs.py::test_workflow_trs_template - location: ('tests/test_trs.py', 107, 'test_workflow_trs_template') - finish pytest_runtest_logfinish --> [] [hook] - pytest_testnodedown [hook] - node: - error: None - finish pytest_testnodedown --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_validate_js.py::test_get_expressions', 'location': ('tests/test_validate_js.py', 24, 'test_get_expressions'), 'keywords': {'test_get_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.6003651379996882, 'start': 1685951467.7454169, 'stop': 1685951468.345769, '$report_type': 'TestReport', 'item_index': 656, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_validate_js.py::test_get_expressions', 'location': ('tests/test_validate_js.py', 24, 'test_get_expressions'), 'keywords': {'test_get_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0020412240000950987, 'start': 1685951468.346211, 'stop': 1685951468.348253, '$report_type': 'TestReport', 'item_index': 656, 'worker_id': 'gw2', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_validate_js.py::test_get_expressions - location: ('tests/test_validate_js.py', 24, 'test_get_expressions') - finish pytest_runtest_logfinish --> [] [hook] - pytest_testnodedown [hook] - node: - error: None - finish pytest_testnodedown --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_dont_require_inputs', 'location': ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs'), 'keywords': {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nusage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\n [-h] --input INPUT [job_order]\n/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script: error: the following arguments are required: --input\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 1.982607547999578, 'start': 1685951466.914974, 'stop': 1685951468.897533, '$report_type': 'TestReport', 'item_index': 644, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_toolargparse.py::test_dont_require_inputs', 'location': ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs'), 'keywords': {'test_dont_require_inputs': 1, 'test_toolargparse.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', '\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nusage: /private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\n [-h] --input INPUT [job_order]\n/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script: error: the following arguments are required: --input\n\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\n\x1b[1;30mDEBUG\x1b[0m \x1b[32mParsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\x1b[0m\n\x1b[1;30mINFO\x1b[0m Final process status is success\n'), ('Captured log call', 'INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": {\n "class": "File",\n "location": "file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script"\n }\n}\nINFO cwltool:main.py:1366 Final process status is success\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nINFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved \'/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\' to \'file:///private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script\'\nDEBUG cwltool:main.py:463 Parsed job order from command line: {\n "id": "/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/pytest-of-jasperk/pytest-54/popen-gw5/test_dont_require_inputs0/script",\n "input": null\n}\nINFO cwltool:main.py:1366 Final process status is success')], 'duration': 0.00028186799954710295, 'start': 1685951468.898069, 'stop': 1685951468.8983521, '$report_type': 'TestReport', 'item_index': 644, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_toolargparse.py::test_dont_require_inputs - location: ('tests/test_toolargparse.py', 143, 'test_dont_require_inputs') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_validate_js.py::test_validate_js_expressions - location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_validate_js.py::test_validate_js_expressions', 'location': ('tests/test_validate_js.py', 36, 'test_validate_js_expressions'), 'keywords': {'test_validate_js_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003742219996638596, 'start': 1685951468.900276, 'stop': 1685951468.900651, '$report_type': 'TestReport', 'item_index': 657, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_validate_js.py::test_validate_js_expressions', 'location': ('tests/test_validate_js.py', 36, 'test_validate_js_expressions'), 'keywords': {'test_validate_js_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:08]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.\x1b[0m\n"), ('Captured log call', "WARNING cwltool:validate_js.py:208 JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.")], 'duration': 0.016739755000344303, 'start': 1685951468.9009879, 'stop': 1685951468.9177291, '$report_type': 'TestReport', 'item_index': 657, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_validate_js.py::test_validate_js_expressions', 'location': ('tests/test_validate_js.py', 36, 'test_validate_js_expressions'), 'keywords': {'test_validate_js_expressions': 1, 'test_validate_js.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stderr call', "\x1b[32m[2023-06-05 09:51:08]\x1b[0m \x1b[1;30mWARNING\x1b[0m \x1b[33m JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.\x1b[0m\n"), ('Captured log call', "WARNING cwltool:validate_js.py:208 JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined.")], 'duration': 0.0022302220004348783, 'start': 1685951468.91821, 'stop': 1685951468.920442, '$report_type': 'TestReport', 'item_index': 657, 'worker_id': 'gw5', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_validate_js.py::test_validate_js_expressions - location: ('tests/test_validate_js.py', 36, 'test_validate_js_expressions') - finish pytest_runtest_logfinish --> [] [hook] - pytest_testnodedown [hook] - node: - error: None - finish pytest_testnodedown --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_schemadef.py::test_schemadef', 'location': ('tests/test_schemadef.py', 7, 'test_schemadef'), 'keywords': {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard")], 'duration': 14.348487793000459, 'start': 1685951454.6698, 'stop': 1685951469.017929, '$report_type': 'TestReport', 'item_index': 578, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_schemadef.py::test_schemadef', 'location': ('tests/test_schemadef.py', 7, 'test_schemadef'), 'keywords': {'test_schemadef': 1, 'test_schemadef.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [('Captured stdout call', '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl is valid CWL.\n'), ('Captured stderr call', "\x1b[1;30mINFO\x1b[0m 3.1\n\x1b[1;30mINFO\x1b[0m Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\ntests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\ntests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\n"), ('Captured log call', "INFO cwltool:main.py:1027 3.1\nINFO cwltool:load_tool.py:102 Resolved '/Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl' to 'file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl'\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:162:25: Warning: Field 'type' references unknown identifier\n 'standardHiCpu', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standardHiCpu\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:410:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:712:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:773:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard\nWARNING salad:ref_resolver.py:1157 tests/wf/schemadef-bug-1473.cwl:892:25: Warning: Field 'type' references unknown identifier\n 'standard', tried\n file:///Users/jasperk/gitlab/cwltool/tests/wf/schemadef-bug-1473.cwl#standard")], 'duration': 0.0002445029995215009, 'start': 1685951469.018733, 'stop': 1685951469.018979, '$report_type': 'TestReport', 'item_index': 578, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_schemadef.py::test_schemadef - location: ('tests/test_schemadef.py', 7, 'test_schemadef') - finish pytest_runtest_logfinish --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_obscuring', 'location': ('tests/test_secrets.py', 24, 'test_obscuring'), 'keywords': {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0003606910004236852, 'start': 1685951469.0202398, 'stop': 1685951469.020601, '$report_type': 'TestReport', 'item_index': 579, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_obscuring', 'location': ('tests/test_secrets.py', 24, 'test_obscuring'), 'keywords': {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.00022766500023863045, 'start': 1685951469.020917, 'stop': 1685951469.021145, '$report_type': 'TestReport', 'item_index': 579, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_obscuring', 'location': ('tests/test_secrets.py', 24, 'test_obscuring'), 'keywords': {'test_obscuring': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.00021421099972940283, 'start': 1685951469.021472, 'stop': 1685951469.021687, '$report_type': 'TestReport', 'item_index': 579, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_secrets.py::test_obscuring - location: ('tests/test_secrets.py', 24, 'test_obscuring') - finish pytest_runtest_logstart --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logreport [hook] - report: - pytest_report_teststatus [hook] - report: - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_secrets.py::test_obscuring - location: ('tests/test_secrets.py', 24, 'test_obscuring') - finish pytest_runtest_logfinish --> [] [hook] - pytest_runtest_logstart [hook] - nodeid: tests/test_secrets.py::test_secrets[-hello bar] - location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') - finish pytest_runtest_logstart --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secrets[-hello bar]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]'), 'keywords': {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'setup', 'user_properties': [], 'sections': [], 'duration': 0.0005970800002614851, 'start': 1685951469.022847, 'stop': 1685951469.023445, '$report_type': 'TestReport', 'item_index': 580, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> -hello bar]' when='setup' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -hello bar]' when='setup' outcome='passed'> - pytest_report_teststatus [hook] - report: -hello bar]' when='setup' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secrets[-hello bar]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]'), 'keywords': {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'call', 'user_properties': [], 'sections': [], 'duration': 0.0002542570000514388, 'start': 1685951469.023823, 'stop': 1685951469.0240781, '$report_type': 'TestReport', 'item_index': 580, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> -hello bar]' when='call' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -hello bar]' when='call' outcome='passed'> - pytest_report_teststatus [hook] - report: -hello bar]' when='call' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('passed', '.', 'PASSED') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_report_from_serializable [hook] - config: <_pytest.config.Config object at 0x11074ef80> - data: {'nodeid': 'tests/test_secrets.py::test_secrets[-hello bar]', 'location': ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]'), 'keywords': {'test_secrets[-hello bar]': 1, 'parametrize': 1, 'pytestmark': 1, '-hello bar': 1, 'test_secrets.py': 1, 'tests/__init__.py': 1, 'cwltool': 1}, 'outcome': 'passed', 'longrepr': None, 'when': 'teardown', 'user_properties': [], 'sections': [], 'duration': 0.0006589340000573429, 'start': 1685951469.0244741, 'stop': 1685951469.025135, '$report_type': 'TestReport', 'item_index': 580, 'worker_id': 'gw0', 'testrun_uid': 'ca4970838f1b415dbaafd06f56809891'} - finish pytest_report_from_serializable --> -hello bar]' when='teardown' outcome='passed'> [hook] - pytest_runtest_logreport [hook] - report: -hello bar]' when='teardown' outcome='passed'> - pytest_report_teststatus [hook] - report: -hello bar]' when='teardown' outcome='passed'> - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_report_teststatus --> ('', '', '') [hook] - finish pytest_runtest_logreport --> [] [hook] - pytest_runtest_logfinish [hook] - nodeid: tests/test_secrets.py::test_secrets[-hello bar] - location: ('tests/test_secrets.py', 40, 'test_secrets[-hello bar]') - finish pytest_runtest_logfinish --> [] [hook] - pytest_testnodedown [hook] - node: - error: None - finish pytest_testnodedown --> [] [hook] - pytest_keyboard_interrupt [hook] - excinfo: - finish pytest_keyboard_interrupt --> [] [hook] - pytest_sessionfinish [hook] - session: testsfailed=6 testscollected=664> - exitstatus: 2 - finish pytest_sessionfinish --> [] [hook] - pytest_unconfigure [hook] - config: <_pytest.config.Config object at 0x11074ef80> - finish pytest_unconfigure --> [] [hook] From c559952b8c40184264359c97689b15cb3e225629 Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Thu, 15 Jun 2023 08:00:30 +0200 Subject: [PATCH 03/34] make clean formatting --- cwltool/argparser.py | 8 ++++---- cwltool/cwlprov/__init__.py | 5 +++-- cwltool/cwlprov/provenance_profile.py | 4 ++-- cwltool/cwlprov/ro.py | 16 +++++++++++++--- cwltool/executors.py | 4 +++- cwltool/job.py | 5 ++++- cwltool/main.py | 3 ++- 7 files changed, 31 insertions(+), 14 deletions(-) diff --git a/cwltool/argparser.py b/cwltool/argparser.py index 60050ff5e..dbb8349b4 100644 --- a/cwltool/argparser.py +++ b/cwltool/argparser.py @@ -289,19 +289,19 @@ def arg_parser() -> argparse.ArgumentParser: # TO DO: Not yet implemented provgroup.add_argument( - "--no-data", # Maybe change to no-input and no-intermediate to ignore those kind of files?... + "--no-data", # Maybe change to no-input and no-intermediate to ignore those kind of files?... default=False, action="store_true", - help="Disables the storage of input and output data files of the workflow in the provenance data folder", + help="Disables the storage of input and output data files", dest="no_data", ) # TO DO: Not yet implemented provgroup.add_argument( - "--no-input", # Maybe change to no-input and no-intermediate to ignore those kind of files?... + "--no-input", # Maybe change to no-input and no-intermediate to ignore those kind of files?... default=False, action="store_true", - help="Disables the storage of input and output data files of the workflow in the provenance data folder", + help="Disables the storage of input data files", dest="no_input", ) diff --git a/cwltool/cwlprov/__init__.py b/cwltool/cwlprov/__init__.py index 78663ae4c..8ffcff4c3 100644 --- a/cwltool/cwlprov/__init__.py +++ b/cwltool/cwlprov/__init__.py @@ -6,7 +6,7 @@ import re import uuid from getpass import getuser -from typing import IO, Any, Callable, Dict, List, Optional, Tuple, Union +from typing import IO, Any, Dict, List, Optional, Tuple, Union from typing_extensions import TypedDict @@ -14,6 +14,7 @@ from ..loghandler import _logger + def _whoami() -> Tuple[str, str]: """Return the current operating system account as (username, fullname).""" username = getuser() @@ -197,4 +198,4 @@ def content_processor( contents = src_file.read(buffersize) if dst_file is not None: dst_file.flush() - return checksum.hexdigest().lower() \ No newline at end of file + return checksum.hexdigest().lower() diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 609d9523e..289b9e6d0 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -29,7 +29,7 @@ from ..loghandler import _logger from ..process import Process, shortname from ..stdfsaccess import StdFsAccess -from ..utils import CWLObjectType, JobsType, get_listing, posix_path, versionstring +from ..utils import CWLObjectType, JobsType, posix_path, versionstring from ..workflow_job import WorkflowJob from .provenance_constants import ( ACCOUNT_UUID, @@ -606,7 +606,7 @@ def used_artefacts( job_order: Union[CWLObjectType, List[CWLObjectType]], process_run_id: str, name: Optional[str] = None, - load_listing = None, + load_listing=None, ) -> None: """Add used() for each data artefact.""" if isinstance(job_order, list): diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index f819113e9..307e5c569 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -34,7 +34,15 @@ posix_path, versionstring, ) -from . import Aggregate, Annotation, AuthoredBy, _valid_orcid, _whoami, checksum_copy, checksum_only +from . import ( + Aggregate, + Annotation, + AuthoredBy, + _valid_orcid, + _whoami, + checksum_copy, + checksum_only, +) from .provenance_constants import ( ACCOUNT_UUID, CWLPROV_VERSION, @@ -508,8 +516,10 @@ def add_data_file( _logger.warning("[provenance] Unknown hash method %s for bagit manifest", Hasher) # Inefficient, bagit support need to checksum again self._add_to_bagit(rel_path) - if 'dir' in self.relativised_input_object: - _logger.debug("[provenance] Directory :%s", self.relativised_input_object['dir']['basename']) + if "dir" in self.relativised_input_object: + _logger.debug( + "[provenance] Directory :%s", self.relativised_input_object["dir"]["basename"] + ) else: _logger.debug("[provenance] Added data file %s", path) if timestamp is not None: diff --git a/cwltool/executors.py b/cwltool/executors.py index 6310c2005..2585daad5 100644 --- a/cwltool/executors.py +++ b/cwltool/executors.py @@ -172,7 +172,9 @@ def check_for_abstract_op(tool: CWLObjectType) -> None: ): process_run_id: Optional[str] = None name = "primary" - process.parent_wf.generate_output_prov(self.final_output[0], process_run_id, name) # Note to self... # , "generate_output_prov") + process.parent_wf.generate_output_prov( + self.final_output[0], process_run_id, name + ) # Note to self... # , "generate_output_prov") process.parent_wf.document.wasEndedBy( process.parent_wf.workflow_run_uri, None, diff --git a/cwltool/job.py b/cwltool/job.py index a90b99e93..c76f588fd 100644 --- a/cwltool/job.py +++ b/cwltool/job.py @@ -285,7 +285,10 @@ def _execute( and isinstance(job_order, (list, dict)) ): runtimeContext.prov_obj.used_artefacts( - job_order, runtimeContext.process_run_id, str(self.name), load_listing=self.builder.loadListing + job_order, + runtimeContext.process_run_id, + str(self.name), + load_listing=self.builder.loadListing, ) else: _logger.warning( diff --git a/cwltool/main.py b/cwltool/main.py index b670b3f36..926917b75 100755 --- a/cwltool/main.py +++ b/cwltool/main.py @@ -1147,7 +1147,8 @@ def main( temp_workflow_dir = tempfile.TemporaryDirectory() os.makedirs(temp_workflow_dir.name, exist_ok=True) workflow_provenance = temp_workflow_dir.name + "/workflow.ttl" - # Sets up a turtle file for the workflow information (not yet in the provenance folder as it does + # Sets up a turtle file for the workflow information + # (not yet in the provenance folder as it does # not exist and creating it will give issues). output = open(workflow_provenance, "w") _logger.info("Writing workflow rdf to %s", workflow_provenance) From c62979a8f4b336910bbac90e6c098b932707e7e2 Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Thu, 15 Jun 2023 08:01:02 +0200 Subject: [PATCH 04/34] Improved naming for the no_listing test and a creation step of 10.000 files for performance testing --- tests/test_provenance.py | 52 +++++++++++++++++-------------- tests/wf/directory_no_listing.cwl | 10 +++--- 2 files changed, 33 insertions(+), 29 deletions(-) diff --git a/tests/test_provenance.py b/tests/test_provenance.py index c4c23e94c..eb0e2e250 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -209,6 +209,7 @@ def test_directory_workflow(tmp_path: Path) -> None: # List content list_files(tmp_path) + @needs_docker def test_no_data_files(tmp_path: Path) -> None: folder = cwltool( @@ -791,21 +792,17 @@ def test_research_object_picklability(research_object: ResearchObject) -> None: assert pickle.dumps(research_object) is not None - -### Jasper - -import os - +# Function to list filestructure def list_files(startpath): startpath = str(startpath) print("Root: ", startpath) - for root, dirs, files in os.walk(startpath): - level = root.replace(startpath, '').count(os.sep) - indent = ' ' * 4 * (level) - print('{}{}/'.format(indent, os.path.basename(root))) - subindent = ' ' * 4 * (level + 1) + for root, _dirs, files in os.walk(startpath): + level = root.replace(startpath, "").count(os.sep) + indent = " " * 4 * (level) + print("{}{}/".format(indent, os.path.basename(root))) + subindent = " " * 4 * (level + 1) for f in files: - print('{}{}'.format(subindent, f)) + print("{}{}".format(subindent, f)) @needs_docker @@ -850,6 +847,12 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: # Make test files with predictable hashes with open(dir3 / x, "w", encoding="ascii") as f: f.write(x) + # Temporarily generate 10.000 files to test performance + for i in range(10000): + with open(dir3 / f"{x}_{i}", "w", encoding="ascii") as f: + f.write(x) + print("Created 10.000 files in dir_no_listing") + # list_files(dir3) dir4 = tmp_path / "dir_no_info" dir4.mkdir() @@ -862,16 +865,16 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: folder = cwltool( tmp_path, get_data("tests/wf/directory_no_listing.cwl"), - "--dir", + "--dir_deep_listing", str(dir2), - "--ignore", + "--dir_no_listing", str(dir3), - "--ignore_no_info", + "--dir_no_info", str(dir4), ) # Visualize the path structure - list_files(tmp_path) + # list_files(tmp_path) # Output should include ls stdout of filenames a b c on each line file_list = ( @@ -888,18 +891,19 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: # Input files should be captured by hash value, # even if they were inside a class: Directory - for (l, l_hash) in sha1.items(): - prefix = l_hash[:2] # first 2 letters - p = folder / "data" / prefix / l_hash + for f, file_hash in sha1.items(): + prefix = file_hash[:2] # first 2 letters + p = folder / "data" / prefix / file_hash # File should be empty and in the future not existing... # assert os.path.getsize(p.absolute()) == 0 # To be discared when file really does not exist anymore - if l in ['d', 'e', 'f', 'g', 'h', 'i']: - print(f"Analysing file {l}") - assert not p.is_file(), f"Could find {l} as {p}" + if f in ["d", "e", "f", "g", "h", "i"]: + print(f"Analysing file {f}") + assert not p.is_file(), f"Could find {f} as {p}" else: - print(f"Analysing file {l}") - assert p.is_file(), f"Could not find {l} as {p}" + print(f"Analysing file {f}") + assert p.is_file(), f"Could not find {f} as {p}" + def cwltool_no_data(tmp_path: Path, *args: Any) -> Path: prov_folder = tmp_path / "provenance" @@ -912,4 +916,4 @@ def cwltool_no_data(tmp_path: Path, *args: Any) -> Path: with working_directory(tmp_dir): status = main(new_args) assert status == 0, f"Failed: cwltool.main({args})" - return prov_folder \ No newline at end of file + return prov_folder diff --git a/tests/wf/directory_no_listing.cwl b/tests/wf/directory_no_listing.cwl index 0375baa39..f261361e1 100644 --- a/tests/wf/directory_no_listing.cwl +++ b/tests/wf/directory_no_listing.cwl @@ -11,21 +11,21 @@ hints: dockerPull: docker.io/debian:stable-slim inputs: - dir: + dir_deep_listing: type: Directory loadListing: deep_listing - ignore: + dir_no_listing: type: Directory loadListing: no_listing - ignore_no_info: + dir_no_info: type: Directory steps: ls: in: - dir: dir - ignore: ignore + dir: dir_deep_listing + ignore: dir_no_listing out: [listing] run: From bc85a1f80bfe1062944b69a67dc5e56873f01a20 Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Fri, 16 Jun 2023 08:51:56 +0200 Subject: [PATCH 05/34] Identifying what it is processing for provenance --- cwltool/builder.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/cwltool/builder.py b/cwltool/builder.py index ea2a708a6..3d781db9b 100644 --- a/cwltool/builder.py +++ b/cwltool/builder.py @@ -572,6 +572,10 @@ def addsf( datum = cast(CWLObjectType, datum) ll = schema.get("loadListing") or self.loadListing if ll and ll != "no_listing": + # Debug show + for k in datum: + _logger.debug("Datum: %s: %s" % (k, datum[k])) + _logger.debug("----------------------------------------") get_listing( self.fs_access, datum, From 9a6f4ce8095ba88ffc7a68e42521359edf353340 Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Fri, 16 Jun 2023 18:01:11 +0200 Subject: [PATCH 06/34] For the provenance a --no-input option to not copy input files into the provenance directory --- cwltool/cwlprov/ro.py | 8 +++++--- cwltool/main.py | 1 + 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 307e5c569..47089a8af 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -75,6 +75,7 @@ def __init__( orcid: str = "", full_name: str = "", no_data: bool = False, + no_input: bool = False, ) -> None: """Initialize the ResearchObject.""" self.temp_prefix = temp_prefix_ro @@ -98,6 +99,7 @@ def __init__( self.has_manifest = False self.relativised_input_object: CWLObjectType = {} self.no_data = no_data + self.no_input = no_input self._initialize() _logger.debug("[provenance] Temporary research object: %s", self.folder) @@ -190,8 +192,8 @@ def add_tagfile(self, path: str, timestamp: Optional[datetime.datetime] = None) # Below probably OK for now as metadata files # are not too large..? - if self.no_data: - _logger.warning("NO DATA TO BE CAPTURED!!!") + if self.no_input: + _logger.debug("NO INPUT DATA TO BE CAPTURED!!!") checksums[SHA1] = checksum_only(tag_file, hasher=hashlib.sha1) tag_file.seek(0) @@ -585,7 +587,7 @@ def _add_to_bagit(self, rel_path: str, **checksums: str) -> None: checksums = dict(checksums) with open(lpath, "rb") as file_path: # FIXME: Need sha-256 / sha-512 as well for Research Object BagIt profile? - if self.no_data: + if self.data_option: checksums[SHA1] = checksum_only(file_path, hasher=hashlib.sha1) else: checksums[SHA1] = checksum_copy(file_path, hasher=hashlib.sha1) diff --git a/cwltool/main.py b/cwltool/main.py index 926917b75..999e9f743 100755 --- a/cwltool/main.py +++ b/cwltool/main.py @@ -695,6 +695,7 @@ def setup_provenance( orcid=args.orcid, full_name=args.cwl_full_name, no_data=args.no_data, + no_input=args.no_input, ) runtimeContext.research_obj = ro log_file_io = open_log_file_for_activity(ro, ro.engine_uuid) From 456b26cbf1abcd173a8f0a20d63c2cab31a272ed Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Fri, 16 Jun 2023 18:01:31 +0200 Subject: [PATCH 07/34] A work in progress to ensure the test works for no-listing and no-input --- tests/test_provenance.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/tests/test_provenance.py b/tests/test_provenance.py index eb0e2e250..0f6542e91 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -811,6 +811,8 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: This test will check for 3 files that should be there and 3 files that should not be there. @param tmp_path: """ + # TODO no data is currently manually set + data_option = "--no-input" sha1 = { # Expected hashes of ASCII letters (no linefeed) @@ -862,8 +864,14 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: with open(dir4 / x, "w", encoding="ascii") as f: f.write(x) + # Run the workflow folder = cwltool( tmp_path, + # CWL Arguments + "--debug", + # No data argument based on boolean + data_option, + # Workflow arguments get_data("tests/wf/directory_no_listing.cwl"), "--dir_deep_listing", str(dir2), From b278f58b6a62c85accb05acf8ce57b538f4e43ac Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Sun, 18 Jun 2023 10:43:37 +0200 Subject: [PATCH 08/34] Wokring on specifying input/output for provenance --- cwltool/cwlprov/provenance_constants.py | 7 +- cwltool/cwlprov/provenance_profile.py | 27 +++--- cwltool/cwlprov/ro.py | 50 ++++++++--- cwltool/cwlprov/writablebagfile.py | 4 +- tests/test_provenance.py | 114 +++++++++++++++++++----- tests/wf/directory_no_listing.cwl | 16 ++-- 6 files changed, 167 insertions(+), 51 deletions(-) diff --git a/cwltool/cwlprov/provenance_constants.py b/cwltool/cwlprov/provenance_constants.py index ec047df38..c1f2fb31b 100644 --- a/cwltool/cwlprov/provenance_constants.py +++ b/cwltool/cwlprov/provenance_constants.py @@ -18,7 +18,12 @@ # Research Object folders METADATA = "metadata" -DATA = "data" +# sub-folders for data +DATA = "data/input" +INPUT_DATA = "data/input" +INTM_DATA = "data/intermediate" +OUTPUT_DATA = "data/output" + WORKFLOW = "workflow" SNAPSHOT = "snapshot" # sub-folders diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 289b9e6d0..993102452 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -24,13 +24,7 @@ from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity from schema_salad.sourceline import SourceLine -from ..errors import WorkflowException -from ..job import CommandLineJob, JobBase -from ..loghandler import _logger -from ..process import Process, shortname -from ..stdfsaccess import StdFsAccess -from ..utils import CWLObjectType, JobsType, posix_path, versionstring -from ..workflow_job import WorkflowJob +from . import provenance_constants from .provenance_constants import ( ACCOUNT_UUID, CWLPROV, @@ -47,9 +41,16 @@ UUID, WF4EVER, WFDESC, - WFPROV, + WFPROV, DATA, ) from .writablebagfile import create_job, write_bag_file # change this later +from ..errors import WorkflowException +from ..job import CommandLineJob, JobBase +from ..loghandler import _logger +from ..process import Process, shortname +from ..stdfsaccess import StdFsAccess +from ..utils import CWLObjectType, JobsType, posix_path, versionstring +from ..workflow_job import WorkflowJob if TYPE_CHECKING: from .ro import ResearchObject @@ -302,7 +303,8 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st if "checksum" in value: csum = cast(str, value["checksum"]) (method, checksum) = csum.split("$", 1) - if method == SHA1 and self.research_object.has_data_file(checksum): + # TODO Input, intermediate or output file?... + if method == SHA1 and self.research_object.has_data_file(provenance_constants.DATA, checksum): entity = self.document.entity("data:" + checksum) if not entity and "location" in value: @@ -637,7 +639,12 @@ def generate_output_prov( process_run_id: Optional[str], name: Optional[str], ) -> None: - """Call wasGeneratedBy() for each output,copy the files into the RO.""" + """Call wasGeneratedBy() for each output, copy the files into the RO.""" + + # TODO: Change INPUT_DATA to OUTPUT_DATA? + provenance_constants.DATA = provenance_constants.OUTPUT_DATA + x = provenance_constants.DATA + if isinstance(final_output, MutableSequence): for entry in final_output: self.generate_output_prov(entry, process_run_id, name) diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 47089a8af..73b29ce59 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -41,12 +41,11 @@ _valid_orcid, _whoami, checksum_copy, - checksum_only, + checksum_only, provenance_constants, ) from .provenance_constants import ( ACCOUNT_UUID, CWLPROV_VERSION, - DATA, ENCODING, FOAF, LOGS, @@ -101,9 +100,13 @@ def __init__( self.no_data = no_data self.no_input = no_input + # TODO Fix...? Set the INPUT_DATA to default for input + # modify_data("data/inputs") + self._initialize() _logger.debug("[provenance] Temporary research object: %s", self.folder) + def self_check(self) -> None: """Raise ValueError if this RO is closed.""" if self.closed: @@ -119,7 +122,9 @@ def __str__(self) -> str: def _initialize(self) -> None: for research_obj_folder in ( METADATA, - DATA, + provenance_constants.INPUT_DATA, + provenance_constants.INTM_DATA, + provenance_constants.OUTPUT_DATA, WORKFLOW, SNAPSHOT, PROVENANCE, @@ -477,9 +482,9 @@ def generate_snapshot(self, prov_dep: CWLObjectType) -> None: else: pass - def has_data_file(self, sha1hash: str) -> bool: + def has_data_file(self, location: str, sha1hash: str) -> bool: """Confirm the presence of the given file in the RO.""" - folder = os.path.join(self.folder, DATA, sha1hash[0:2]) + folder = os.path.join(self.folder, location, sha1hash[0:2]) hash_path = os.path.join(folder, sha1hash) return os.path.isfile(hash_path) @@ -490,20 +495,37 @@ def add_data_file( content_type: Optional[str] = None, ) -> str: """Copy inputs to data/ folder.""" + # TODO: This also copies the outputs?... # TODO Skip if no-input or no-data is used...? self.self_check() tmp_dir, tmp_prefix = os.path.split(self.temp_prefix) with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp: - if self.no_data: + if self.no_data or self.no_input: checksum = checksum_only(from_fp) else: checksum = checksum_copy(from_fp, tmp) # Calculate hash-based file path - folder = os.path.join(self.folder, DATA, checksum[0:2]) + if "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8" in checksum: # This is the hash of an output file + print(provenance_constants.DATA) + x = provenance_constants.DATA + debug_stop = True + folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) path = os.path.join(folder, checksum) # os.rename assumed safe, as our temp file should # be in same file system as our temp folder + + # Which files end up here? input, intermediate and output files? + + # Test if no-input or no-data is used + # if self.no_data or self.no_input: + # path = tmp.name + + # Obtain the content of tmp.name for debugging + with open(tmp.name, "rb") as f: + content = f.read() + print(">>>", content) + if not os.path.isdir(folder): os.makedirs(folder) os.rename(tmp.name, path) @@ -530,6 +552,9 @@ def add_data_file( Aggregate, {"createdOn": createdOn, "createdBy": createdBy} ) _logger.debug("[provenance] Relative path for data file %s", rel_path) + # This is an output hash + if "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8" in rel_path: + debug_stop = True if content_type is not None: self._content_types[rel_path] = content_type @@ -598,6 +623,8 @@ def _relativise_files( self, structure: Union[CWLObjectType, CWLOutputType, MutableSequence[CWLObjectType]], ) -> None: + # TODO - Are there only input files arriving here? + """Save any file objects into the RO and update the local paths.""" # Base case - we found a File we need to update _logger.debug("[provenance] Relativising: %s", structure) @@ -612,14 +639,17 @@ def _relativise_files( raise TypeError( f"Only SHA1 CWL checksums are currently supported: {structure}" ) - if self.has_data_file(checksum): + if "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8" in checksum: + x = provenance_constants.DATA + debug_stop = True + if self.has_data_file(provenance_constants.DATA, checksum): prefix = checksum[0:2] - relative_path = PurePosixPath("data") / prefix / checksum + relative_path = PurePosixPath("data/input") / prefix / checksum if not (relative_path is not None and "location" in structure): # Register in RO; but why was this not picked # up by used_artefacts? - _logger.info("[provenance] Adding to RO %s", structure["location"]) + _logger.info("[provenance] Adding to RO '%s' > %s", structure["basename"], structure["location"]) with self.fsaccess.open(cast(str, structure["location"]), "rb") as fp: relative_path = self.add_data_file(fp) checksum = PurePosixPath(relative_path).name diff --git a/cwltool/cwlprov/writablebagfile.py b/cwltool/cwlprov/writablebagfile.py index d5ff3c731..8c1f9d7e2 100644 --- a/cwltool/cwlprov/writablebagfile.py +++ b/cwltool/cwlprov/writablebagfile.py @@ -244,7 +244,9 @@ def create_job( """Generate the new job object with RO specific relative paths.""" copied = copy.deepcopy(builder_job) relativised_input_objecttemp: CWLObjectType = {} - research_object._relativise_files(copied) + # No inputs when either no_input or no_data is True + if not research_object.no_input and not research_object.no_data: + research_object._relativise_files(copied) def jdefault(o: Any) -> Dict[Any, Any]: return dict(o) diff --git a/tests/test_provenance.py b/tests/test_provenance.py index 0f6542e91..9cdd1fe2d 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -191,6 +191,7 @@ def test_directory_workflow(tmp_path: Path) -> None: file_list = ( folder / "data" + / "output" / "3c" / "3ca69e8d6c234a469d16ac28a4a658c92267c423" # checksum as returned from: @@ -203,7 +204,7 @@ def test_directory_workflow(tmp_path: Path) -> None: # even if they were inside a class: Directory for letter, l_hash in sha1.items(): prefix = l_hash[:2] # first 2 letters - p = folder / "data" / prefix / l_hash + p = folder / "data" / "output" / prefix / l_hash assert p.is_file(), f"Could not find {letter} as {p}" # List content @@ -222,7 +223,7 @@ def test_no_data_files(tmp_path: Path) -> None: def check_output_object(base_path: Path) -> None: output_obj = base_path / "workflow" / "primary-output.json" compare_checksum = "sha1$b9214658cc453331b62c2282b772a5c063dbd284" - compare_location = "../data/b9/b9214658cc453331b62c2282b772a5c063dbd284" + compare_location = "../data/input/b9/b9214658cc453331b62c2282b772a5c063dbd284" with open(output_obj) as fp: out_json = json.load(fp) f1 = out_json["sorted_output"] @@ -234,13 +235,14 @@ def check_secondary_files(base_path: Path) -> None: foo_data = ( base_path / "data" + / "input" / "0b" / "0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33" # checksum as returned from: # $ echo -n foo | sha1sum # 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 - ) - bar_data = base_path / "data" / "62" / "62cdb7020ff920e5aa642c3d4066950dd1f01f4d" + bar_data = base_path / "data" / "input" / "62" / "62cdb7020ff920e5aa642c3d4066950dd1f01f4d" assert foo_data.is_file(), "Did not capture file.txt 'foo'" assert bar_data.is_file(), "Did not capture secondary file.txt.idx 'bar" @@ -249,13 +251,13 @@ def check_secondary_files(base_path: Path) -> None: job_json = json.load(fp) # TODO: Verify secondaryFile in primary-job.json f1 = job_json["file1"] - assert f1["location"] == "../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33" + assert f1["location"] == "../data/input/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33" assert f1["basename"] == "foo1.txt" secondaries = f1["secondaryFiles"] assert secondaries f1idx = secondaries[0] - assert f1idx["location"] == "../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d" + assert f1idx["location"] == "../data/input/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d" assert f1idx["basename"], "foo1.txt.idx" @@ -811,9 +813,63 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: This test will check for 3 files that should be there and 3 files that should not be there. @param tmp_path: """ - # TODO no data is currently manually set - data_option = "--no-input" + sha1, dir2, dir3, dir4 = prepare_input_files(tmp_path) + + # Run the workflow + folder = cwltool( + tmp_path, + # CWL Arguments + "--debug", + # Workflow arguments + get_data("tests/wf/directory_no_listing.cwl"), + "--dir_deep_listing", + str(dir2), + "--dir_no_listing", + str(dir3), + "--dir_no_info", + str(dir4), + ) + + # Visualize the path structure + list_files(tmp_path) + + # Output should include ls stdout of filenames a b c on each line + file_list = ( + folder + / "data" + / "output" + / "3c" + / "3ca69e8d6c234a469d16ac28a4a658c92267c423" + # checksum as returned from: + # echo -e "a\nb\nc" | sha1sum + # 3ca69e8d6c234a469d16ac28a4a658c92267c423 - + # , + # folder + # / "data" + # / "input" + # / "c6" + # / "c632ab5419b6b03f3fd31a0d29e70148c675bd80" + ) + + assert file_list.is_file() + + # Input files should be captured by hash value, + # even if they were inside a class: Directory + for f, file_hash in sha1.items(): + prefix = file_hash[:2] # first 2 letters + p = folder / "data" / "input" / prefix / file_hash + # File should be empty and in the future not existing... + # assert os.path.getsize(p.absolute()) == 0 + # To be discared when file really does not exist anymore + if f in ["d", "e", "f", "g", "h", "i"]: + print(f"Analysing file {f}") + assert not p.is_file(), f"Could find {f} as {p}" + else: + print(f"Analysing file {f}") + assert p.is_file(), f"Could not find {f} as {p}" + +def prepare_input_files(tmp_path: Path) -> None: sha1 = { # Expected hashes of ASCII letters (no linefeed) # as returned from: @@ -850,10 +906,10 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: with open(dir3 / x, "w", encoding="ascii") as f: f.write(x) # Temporarily generate 10.000 files to test performance - for i in range(10000): - with open(dir3 / f"{x}_{i}", "w", encoding="ascii") as f: - f.write(x) - print("Created 10.000 files in dir_no_listing") + # for i in range(10): # 000): + # with open(dir3 / f"{x}_{i}", "w", encoding="ascii") as f: + # f.write(x) + # print("Created 10.000 files in dir_no_listing") # list_files(dir3) dir4 = tmp_path / "dir_no_info" @@ -864,6 +920,21 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: with open(dir4 / x, "w", encoding="ascii") as f: f.write(x) + return sha1, dir2, dir3, dir4 + + +@needs_docker +def test_directory_workflow_no_listing_no_input(tmp_path: Path) -> None: + """ + This test will check for 3 files that should be there and 3 files that should not be there. + In addition it will not copy the input files due to the --no-input flag. + @param tmp_path: + """ + # TODO no data is currently manually set + data_option = "--no-input" + + sha1, dir2, dir3, dir4 = prepare_input_files(tmp_path) + # Run the workflow folder = cwltool( tmp_path, @@ -888,6 +959,7 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: file_list = ( folder / "data" + / "output" / "84" / "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4" # checksum as returned from: @@ -897,20 +969,20 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: assert file_list.is_file() - # Input files should be captured by hash value, - # even if they were inside a class: Directory + # Input files should be in the provenance location for f, file_hash in sha1.items(): prefix = file_hash[:2] # first 2 letters p = folder / "data" / prefix / file_hash - # File should be empty and in the future not existing... - # assert os.path.getsize(p.absolute()) == 0 - # To be discared when file really does not exist anymore - if f in ["d", "e", "f", "g", "h", "i"]: - print(f"Analysing file {f}") - assert not p.is_file(), f"Could find {f} as {p}" + + if p.is_file(): + print("!!!!", os.path.getsize(p)) + print(f"Analysing file '{f}' '{p}'") + with open(p, "r", encoding="ascii") as f: + content = f.read() + print(f"Content: '{content}'") + assert not p.is_file(), f"Could find '{f}' as '{p}'" else: - print(f"Analysing file {f}") - assert p.is_file(), f"Could not find {f} as {p}" + assert not p.is_file(), f"Could find '{f}' as '{p}'" def cwltool_no_data(tmp_path: Path, *args: Any) -> Path: diff --git a/tests/wf/directory_no_listing.cwl b/tests/wf/directory_no_listing.cwl index f261361e1..b8fce7758 100644 --- a/tests/wf/directory_no_listing.cwl +++ b/tests/wf/directory_no_listing.cwl @@ -36,10 +36,10 @@ steps: type: Directory inputBinding: position: 1 - ignore: - type: Directory - inputBinding: - position: 2 +# ignore: +# type: Directory +# inputBinding: +# position: 2 outputs: listing: type: stdout @@ -59,10 +59,10 @@ steps: - shellQuote: false valueFrom: > pwd; - mkdir -p dir1/a/b; - echo -n a > dir1/a.txt; - echo -n b > dir1/a/b.txt; - echo -n c > dir1/a/b/c.txt; + mkdir -p dir1/x/y; + echo -n x > dir1/x.txt; + echo -n y > dir1/x/y.txt; + echo -n z > dir1/x/y/z.txt; inputs: [] outputs: dir1: From fd14f0d7d7a5c3b754b4ddf91ba5d2a20ede1fbd Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Thu, 22 Jun 2023 15:20:03 +0200 Subject: [PATCH 09/34] working on no-input --- cwltool/cwlprov/provenance_profile.py | 23 +++--- cwltool/cwlprov/ro.py | 113 +++++++++++++------------- tests/test_provenance.py | 15 ++-- 3 files changed, 75 insertions(+), 76 deletions(-) diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 993102452..b843f4a1c 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -24,6 +24,13 @@ from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity from schema_salad.sourceline import SourceLine +from ..errors import WorkflowException +from ..job import CommandLineJob, JobBase +from ..loghandler import _logger +from ..process import Process, shortname +from ..stdfsaccess import StdFsAccess +from ..utils import CWLObjectType, JobsType, posix_path, versionstring +from ..workflow_job import WorkflowJob from . import provenance_constants from .provenance_constants import ( ACCOUNT_UUID, @@ -41,16 +48,9 @@ UUID, WF4EVER, WFDESC, - WFPROV, DATA, + WFPROV, ) from .writablebagfile import create_job, write_bag_file # change this later -from ..errors import WorkflowException -from ..job import CommandLineJob, JobBase -from ..loghandler import _logger -from ..process import Process, shortname -from ..stdfsaccess import StdFsAccess -from ..utils import CWLObjectType, JobsType, posix_path, versionstring -from ..workflow_job import WorkflowJob if TYPE_CHECKING: from .ro import ResearchObject @@ -304,7 +304,10 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st csum = cast(str, value["checksum"]) (method, checksum) = csum.split("$", 1) # TODO Input, intermediate or output file?... - if method == SHA1 and self.research_object.has_data_file(provenance_constants.DATA, checksum): + # if provenance_constants.DATA == 'data/input' + if method == SHA1 and self.research_object.has_data_file( + provenance_constants.DATA, checksum + ): entity = self.document.entity("data:" + checksum) if not entity and "location" in value: @@ -640,10 +643,8 @@ def generate_output_prov( name: Optional[str], ) -> None: """Call wasGeneratedBy() for each output, copy the files into the RO.""" - # TODO: Change INPUT_DATA to OUTPUT_DATA? provenance_constants.DATA = provenance_constants.OUTPUT_DATA - x = provenance_constants.DATA if isinstance(final_output, MutableSequence): for entry in final_output: diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 73b29ce59..062856d5f 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -41,7 +41,8 @@ _valid_orcid, _whoami, checksum_copy, - checksum_only, provenance_constants, + checksum_only, + provenance_constants, ) from .provenance_constants import ( ACCOUNT_UUID, @@ -106,7 +107,6 @@ def __init__( self._initialize() _logger.debug("[provenance] Temporary research object: %s", self.folder) - def self_check(self) -> None: """Raise ValueError if this RO is closed.""" if self.closed: @@ -196,8 +196,8 @@ def add_tagfile(self, path: str, timestamp: Optional[datetime.datetime] = None) # adding checksums after closing. # Below probably OK for now as metadata files # are not too large..? - - if self.no_input: + # x = provenance_constants.DATA + if self.no_input and provenance_constants.DATA == "data/input": _logger.debug("NO INPUT DATA TO BE CAPTURED!!!") checksums[SHA1] = checksum_only(tag_file, hasher=hashlib.sha1) @@ -494,58 +494,56 @@ def add_data_file( timestamp: Optional[datetime.datetime] = None, content_type: Optional[str] = None, ) -> str: - """Copy inputs to data/ folder.""" + """Copy intermediate? inputs to data/ folder.""" + # provenance_constants.DATA = "data/intermediate" # Change to that ??? # TODO: This also copies the outputs?... # TODO Skip if no-input or no-data is used...? self.self_check() tmp_dir, tmp_prefix = os.path.split(self.temp_prefix) - with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp: - if self.no_data or self.no_input: - checksum = checksum_only(from_fp) - else: - checksum = checksum_copy(from_fp, tmp) - - # Calculate hash-based file path - if "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8" in checksum: # This is the hash of an output file - print(provenance_constants.DATA) - x = provenance_constants.DATA - debug_stop = True - folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) - path = os.path.join(folder, checksum) - # os.rename assumed safe, as our temp file should - # be in same file system as our temp folder - - # Which files end up here? input, intermediate and output files? - - # Test if no-input or no-data is used - # if self.no_data or self.no_input: - # path = tmp.name - - # Obtain the content of tmp.name for debugging - with open(tmp.name, "rb") as f: - content = f.read() - print(">>>", content) - - if not os.path.isdir(folder): - os.makedirs(folder) - os.rename(tmp.name, path) - - # Relative posix path - rel_path = posix_path(os.path.relpath(path, self.folder)) - - # Register in bagit checksum - if Hasher == hashlib.sha1: - self._add_to_bagit(rel_path, sha1=checksum) - else: - _logger.warning("[provenance] Unknown hash method %s for bagit manifest", Hasher) - # Inefficient, bagit support need to checksum again - self._add_to_bagit(rel_path) - if "dir" in self.relativised_input_object: - _logger.debug( - "[provenance] Directory :%s", self.relativised_input_object["dir"]["basename"] - ) + if self.no_data: + checksum = checksum_only(from_fp) + # Create rel_path + folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) + path = os.path.join(folder, checksum) + # Relative posix path + rel_path = posix_path(os.path.relpath(path, self.folder)) + elif self.no_input and provenance_constants.DATA == provenance_constants.INPUT_DATA: + checksum = checksum_only(from_fp) + # Create rel_path + folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) + path = os.path.join(folder, checksum) + # Relative posix path + rel_path = posix_path(os.path.relpath(path, self.folder)) else: - _logger.debug("[provenance] Added data file %s", path) + with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp: + checksum = checksum_copy(from_fp, tmp) + folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) + path = os.path.join(folder, checksum) + if not os.path.isdir(folder): + os.makedirs(folder) + # Only rename when neither no data and no input is used + os.rename(tmp.name, path) + _logger.debug("Renaming %s to %s", tmp.name, path) + + # Relative posix path + rel_path = posix_path(os.path.relpath(path, self.folder)) + + # Register in bagit checksum + if Hasher == hashlib.sha1: + self._add_to_bagit(rel_path, sha1=checksum) + else: + _logger.warning( + "[provenance] Unknown hash method %s for bagit manifest", Hasher + ) + # Inefficient, bagit support need to checksum again + self._add_to_bagit(rel_path) + if "dir" in self.relativised_input_object: + _logger.debug( + "[provenance] Directory :%s", + self.relativised_input_object["dir"]["basename"], + ) + else: + _logger.debug("[provenance] Added data file %s", path) if timestamp is not None: createdOn, createdBy = self._self_made(timestamp) self._file_provenance[rel_path] = cast( @@ -553,13 +551,12 @@ def add_data_file( ) _logger.debug("[provenance] Relative path for data file %s", rel_path) # This is an output hash - if "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8" in rel_path: - debug_stop = True if content_type is not None: self._content_types[rel_path] = content_type return rel_path + def _self_made( self, timestamp: Optional[datetime.datetime] = None ) -> Tuple[str, Dict[str, str]]: # createdOn, createdBy @@ -639,9 +636,7 @@ def _relativise_files( raise TypeError( f"Only SHA1 CWL checksums are currently supported: {structure}" ) - if "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8" in checksum: - x = provenance_constants.DATA - debug_stop = True + if self.has_data_file(provenance_constants.DATA, checksum): prefix = checksum[0:2] relative_path = PurePosixPath("data/input") / prefix / checksum @@ -649,7 +644,11 @@ def _relativise_files( if not (relative_path is not None and "location" in structure): # Register in RO; but why was this not picked # up by used_artefacts? - _logger.info("[provenance] Adding to RO '%s' > %s", structure["basename"], structure["location"]) + _logger.info( + "[provenance] Adding to RO '%s' > %s", + structure["basename"], + structure["location"], + ) with self.fsaccess.open(cast(str, structure["location"]), "rb") as fp: relative_path = self.add_data_file(fp) checksum = PurePosixPath(relative_path).name diff --git a/tests/test_provenance.py b/tests/test_provenance.py index 9cdd1fe2d..f06be3c20 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -910,7 +910,7 @@ def prepare_input_files(tmp_path: Path) -> None: # with open(dir3 / f"{x}_{i}", "w", encoding="ascii") as f: # f.write(x) # print("Created 10.000 files in dir_no_listing") - # list_files(dir3) + # list_files(dir3) dir4 = tmp_path / "dir_no_info" dir4.mkdir() @@ -927,7 +927,7 @@ def prepare_input_files(tmp_path: Path) -> None: def test_directory_workflow_no_listing_no_input(tmp_path: Path) -> None: """ This test will check for 3 files that should be there and 3 files that should not be there. - In addition it will not copy the input files due to the --no-input flag. + In addition, it will not copy the input files due to the --no-input flag. @param tmp_path: """ # TODO no data is currently manually set @@ -953,7 +953,7 @@ def test_directory_workflow_no_listing_no_input(tmp_path: Path) -> None: ) # Visualize the path structure - # list_files(tmp_path) + list_files(tmp_path) # Output should include ls stdout of filenames a b c on each line file_list = ( @@ -975,14 +975,13 @@ def test_directory_workflow_no_listing_no_input(tmp_path: Path) -> None: p = folder / "data" / prefix / file_hash if p.is_file(): - print("!!!!", os.path.getsize(p)) - print(f"Analysing file '{f}' '{p}'") + print(f"Analysing file {f!r} {p!r}") with open(p, "r", encoding="ascii") as f: content = f.read() - print(f"Content: '{content}'") - assert not p.is_file(), f"Could find '{f}' as '{p}'" + print(f"Content: {content!r}") + assert not p.is_file(), f"Could find {f!r} as {p!r}" else: - assert not p.is_file(), f"Could find '{f}' as '{p}'" + assert not p.is_file(), f"Could find {f!r} as {p!r}" def cwltool_no_data(tmp_path: Path, *args: Any) -> Path: From 95cff2bdef80535addde63cd39717f9fdfbc1301 Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Thu, 22 Jun 2023 16:55:10 +0200 Subject: [PATCH 10/34] move back from data/input data/output to a data folder to see if RO-Crate can cover that part but still keep the no-input option --- cwltool/cwlprov/provenance_constants.py | 1 + cwltool/cwlprov/provenance_profile.py | 4 ++-- cwltool/cwlprov/ro.py | 8 ++++---- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/cwltool/cwlprov/provenance_constants.py b/cwltool/cwlprov/provenance_constants.py index c1f2fb31b..7e0480e90 100644 --- a/cwltool/cwlprov/provenance_constants.py +++ b/cwltool/cwlprov/provenance_constants.py @@ -20,6 +20,7 @@ METADATA = "metadata" # sub-folders for data DATA = "data/input" +DATAX = "data" INPUT_DATA = "data/input" INTM_DATA = "data/intermediate" OUTPUT_DATA = "data/output" diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index b843f4a1c..33f170ad0 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -48,7 +48,7 @@ UUID, WF4EVER, WFDESC, - WFPROV, + WFPROV, DATAX, ) from .writablebagfile import create_job, write_bag_file # change this later @@ -306,7 +306,7 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st # TODO Input, intermediate or output file?... # if provenance_constants.DATA == 'data/input' if method == SHA1 and self.research_object.has_data_file( - provenance_constants.DATA, checksum + DATAX, checksum ): entity = self.document.entity("data:" + checksum) diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 062856d5f..5583865d4 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -61,7 +61,7 @@ USER_UUID, UUID, WORKFLOW, - Hasher, + Hasher, DATAX, ) @@ -503,21 +503,21 @@ def add_data_file( if self.no_data: checksum = checksum_only(from_fp) # Create rel_path - folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) + folder = os.path.join(self.folder, DATAX, checksum[0:2]) path = os.path.join(folder, checksum) # Relative posix path rel_path = posix_path(os.path.relpath(path, self.folder)) elif self.no_input and provenance_constants.DATA == provenance_constants.INPUT_DATA: checksum = checksum_only(from_fp) # Create rel_path - folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) + folder = os.path.join(self.folder, DATAX, checksum[0:2]) path = os.path.join(folder, checksum) # Relative posix path rel_path = posix_path(os.path.relpath(path, self.folder)) else: with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp: checksum = checksum_copy(from_fp, tmp) - folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) + folder = os.path.join(self.folder, DATAX, checksum[0:2]) path = os.path.join(folder, checksum) if not os.path.isdir(folder): os.makedirs(folder) From cdbf106d16ed9be10ae6363da97226d19607ac4f Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Thu, 22 Jun 2023 16:58:48 +0200 Subject: [PATCH 11/34] Likely missed one --- cwltool/cwlprov/ro.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 5583865d4..0f8dc8532 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -637,7 +637,7 @@ def _relativise_files( f"Only SHA1 CWL checksums are currently supported: {structure}" ) - if self.has_data_file(provenance_constants.DATA, checksum): + if self.has_data_file(DATAX, checksum): prefix = checksum[0:2] relative_path = PurePosixPath("data/input") / prefix / checksum From 4d8ae622f0d579d8489d5be18628a1ab94080c0a Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Thu, 22 Jun 2023 17:10:50 +0200 Subject: [PATCH 12/34] Moved back to provenance_constants.DATA with comments for DATAX to know where the change for switchback could be needed --- cwltool/cwlprov/provenance_profile.py | 2 +- cwltool/cwlprov/ro.py | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 33f170ad0..05888487b 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -306,7 +306,7 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st # TODO Input, intermediate or output file?... # if provenance_constants.DATA == 'data/input' if method == SHA1 and self.research_object.has_data_file( - DATAX, checksum + provenance_constants.DATA, checksum # DATAX ): entity = self.document.entity("data:" + checksum) diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 0f8dc8532..31f534802 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -503,21 +503,21 @@ def add_data_file( if self.no_data: checksum = checksum_only(from_fp) # Create rel_path - folder = os.path.join(self.folder, DATAX, checksum[0:2]) + folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) # DATAX path = os.path.join(folder, checksum) # Relative posix path rel_path = posix_path(os.path.relpath(path, self.folder)) elif self.no_input and provenance_constants.DATA == provenance_constants.INPUT_DATA: checksum = checksum_only(from_fp) # Create rel_path - folder = os.path.join(self.folder, DATAX, checksum[0:2]) + folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) # DATAX path = os.path.join(folder, checksum) # Relative posix path rel_path = posix_path(os.path.relpath(path, self.folder)) else: with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp: checksum = checksum_copy(from_fp, tmp) - folder = os.path.join(self.folder, DATAX, checksum[0:2]) + folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) # DATAX path = os.path.join(folder, checksum) if not os.path.isdir(folder): os.makedirs(folder) @@ -637,7 +637,7 @@ def _relativise_files( f"Only SHA1 CWL checksums are currently supported: {structure}" ) - if self.has_data_file(DATAX, checksum): + if self.has_data_file(provenance_constants.DATA, checksum): # DATAX prefix = checksum[0:2] relative_path = PurePosixPath("data/input") / prefix / checksum From 5fc090b063f430dedd316c62585c7b1d4bb3722e Mon Sep 17 00:00:00 2001 From: Changlin Date: Thu, 14 Mar 2024 14:11:09 +0000 Subject: [PATCH 13/34] fix merge err --- cwltool/cwlprov/__init__.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/cwltool/cwlprov/__init__.py b/cwltool/cwlprov/__init__.py index 4c7ce7f88..7a1c0093c 100644 --- a/cwltool/cwlprov/__init__.py +++ b/cwltool/cwlprov/__init__.py @@ -6,13 +6,7 @@ import re import uuid from getpass import getuser -<<<<<<< HEAD -from typing import IO, Any, Dict, List, Optional, Tuple, Union - -from typing_extensions import TypedDict -======= from typing import IO, Any, Callable, Dict, List, Optional, Tuple, TypedDict, Union ->>>>>>> main from cwltool.cwlprov.provenance_constants import Hasher From 18a9bd6329bd82b4cf68e86dd2ce03b0151c4f2b Mon Sep 17 00:00:00 2001 From: Changlin Date: Fri, 22 Mar 2024 18:22:05 +0000 Subject: [PATCH 14/34] fix loadListing of dir for prov --- cwltool/cwlprov/provenance_profile.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 43d57cc6e..271887f0b 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -29,7 +29,7 @@ from ..loghandler import _logger from ..process import Process, shortname from ..stdfsaccess import StdFsAccess -from ..utils import CWLObjectType, JobsType, posix_path, versionstring +from ..utils import CWLObjectType, JobsType, posix_path, versionstring, get_listing from ..workflow_job import WorkflowJob from . import provenance_constants from .provenance_constants import ( @@ -414,9 +414,12 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: # FIXME: .listing might not be populated yet - hopefully # a later call to this method will sort that is_empty = True - + + # get loadlisting # if "listing" not in value: - # get_listing(self.fsaccess, value) + ll = value.get("loadListing") + if ll and ll != "no_listing": + get_listing(self.fsaccess, value, (ll == "deep_listing")) for entry in cast(MutableSequence[CWLObjectType], value.get("listing", [])): is_empty = False # Declare child-artifacts From fc0e331f8a411dc0e2708b82492f8052d05d0644 Mon Sep 17 00:00:00 2001 From: Changlin Date: Fri, 22 Mar 2024 19:38:26 +0000 Subject: [PATCH 15/34] misc change of comments --- cwltool/cwlprov/provenance_profile.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 271887f0b..385809d3b 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -415,8 +415,7 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: # a later call to this method will sort that is_empty = True - # get loadlisting - # if "listing" not in value: + # get loadlisting, and load the listing if not no_listing, recursively if deep_listing ll = value.get("loadListing") if ll and ll != "no_listing": get_listing(self.fsaccess, value, (ll == "deep_listing")) From 627026c9709a9b52598e79fdd79dc395bafb8c9e Mon Sep 17 00:00:00 2001 From: Changlin Date: Tue, 26 Mar 2024 12:29:38 +0000 Subject: [PATCH 16/34] fix text, remove vscode space files --- cwltool.code-workspace | 8 -------- cwltool/cwlprov/provenance_profile.py | 1 - 2 files changed, 9 deletions(-) delete mode 100644 cwltool.code-workspace diff --git a/cwltool.code-workspace b/cwltool.code-workspace deleted file mode 100644 index 876a1499c..000000000 --- a/cwltool.code-workspace +++ /dev/null @@ -1,8 +0,0 @@ -{ - "folders": [ - { - "path": "." - } - ], - "settings": {} -} \ No newline at end of file diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 385809d3b..39f9c4d86 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -244,7 +244,6 @@ def evaluate( # record provenance of workflow executions self.prospective_prov(job) customised_job = copy_job_order(job, job_order_object) - # Note to self: Listing goes ok here self.used_artefacts(customised_job, self.workflow_run_uri) def record_process_start( From 96d1e2081950b9251c7c421d3130cbe37ecb8532 Mon Sep 17 00:00:00 2001 From: Changlin Date: Tue, 26 Mar 2024 13:27:18 +0000 Subject: [PATCH 17/34] remove redundant texts --- cwltool/executors.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/cwltool/executors.py b/cwltool/executors.py index 89a450e76..bfc87f9c7 100644 --- a/cwltool/executors.py +++ b/cwltool/executors.py @@ -176,9 +176,7 @@ def check_for_abstract_op(tool: CWLObjectType) -> None: ): process_run_id: Optional[str] = None name = "primary" - process.parent_wf.generate_output_prov( - self.final_output[0], process_run_id, name - ) # Note to self... # , "generate_output_prov") + process.parent_wf.generate_output_prov(self.final_output[0], process_run_id, name) process.parent_wf.document.wasEndedBy( process.parent_wf.workflow_run_uri, None, From 88b113be9de22598ca197b5a651add1b2dced9a5 Mon Sep 17 00:00:00 2001 From: Changlin Date: Thu, 11 Apr 2024 16:09:38 +0000 Subject: [PATCH 18/34] minor changes of logging --- cwltool/cwlprov/__init__.py | 2 +- cwltool/cwlprov/provenance_profile.py | 2 +- cwltool/cwlprov/ro.py | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/cwltool/cwlprov/__init__.py b/cwltool/cwlprov/__init__.py index 7a1c0093c..8781a5970 100644 --- a/cwltool/cwlprov/__init__.py +++ b/cwltool/cwlprov/__init__.py @@ -174,7 +174,7 @@ def checksum_only( ) -> str: """Calculate the checksum only, does not copy the data files.""" if dst_file is not None: - _logger.error("Destination file should be None but it is %s", dst_file) + _logger.error("[Debug Checksum Only] Destination file should be None but it is %s", dst_file) """Compute checksums while copying a file.""" # TODO: Use hashlib.new(Hasher_str) instead? checksum = hasher() diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 39f9c4d86..271ed46fd 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -29,7 +29,7 @@ from ..loghandler import _logger from ..process import Process, shortname from ..stdfsaccess import StdFsAccess -from ..utils import CWLObjectType, JobsType, posix_path, versionstring, get_listing +from ..utils import CWLObjectType, JobsType, get_listing, posix_path, versionstring from ..workflow_job import WorkflowJob from . import provenance_constants from .provenance_constants import ( diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 20afca67b..34006f690 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -498,7 +498,7 @@ def add_data_file( """Copy intermediate? inputs to data/ folder.""" # provenance_constants.DATA = "data/intermediate" # Change to that ??? # TODO: This also copies the outputs?... - # TODO Skip if no-input or no-data is used...? + # TODO Skip if no-input or no-data is used self.self_check() tmp_dir, tmp_prefix = os.path.split(self.temp_prefix) if self.no_data: @@ -610,7 +610,7 @@ def _add_to_bagit(self, rel_path: str, **checksums: str) -> None: checksums = dict(checksums) with open(lpath, "rb") as file_path: # FIXME: Need sha-256 / sha-512 as well for Research Object BagIt profile? - if self.data_option: + if self.no_data or self.no_input: checksums[SHA1] = checksum_only(file_path, hasher=hashlib.sha1) else: checksums[SHA1] = checksum_copy(file_path, hasher=hashlib.sha1) From c979e297bce67c66ea7499ef4476a9f8c9e1c5ef Mon Sep 17 00:00:00 2001 From: Jasper Koehorst Date: Wed, 17 Apr 2024 08:46:27 +0200 Subject: [PATCH 19/34] Result of make cleanup --- cwltool/cwlprov/__init__.py | 6 ++++-- cwltool/cwlprov/provenance_constants.py | 2 +- cwltool/cwlprov/provenance_profile.py | 10 +++++----- cwltool/cwlprov/ro.py | 15 ++++++++------- 4 files changed, 18 insertions(+), 15 deletions(-) diff --git a/cwltool/cwlprov/__init__.py b/cwltool/cwlprov/__init__.py index 8781a5970..fe91037a0 100644 --- a/cwltool/cwlprov/__init__.py +++ b/cwltool/cwlprov/__init__.py @@ -6,7 +6,7 @@ import re import uuid from getpass import getuser -from typing import IO, Any, Callable, Dict, List, Optional, Tuple, TypedDict, Union +from typing import IO, Any, Dict, List, Optional, Tuple, TypedDict, Union from cwltool.cwlprov.provenance_constants import Hasher @@ -174,7 +174,9 @@ def checksum_only( ) -> str: """Calculate the checksum only, does not copy the data files.""" if dst_file is not None: - _logger.error("[Debug Checksum Only] Destination file should be None but it is %s", dst_file) + _logger.error( + "[Debug Checksum Only] Destination file should be None but it is %s", dst_file + ) """Compute checksums while copying a file.""" # TODO: Use hashlib.new(Hasher_str) instead? checksum = hasher() diff --git a/cwltool/cwlprov/provenance_constants.py b/cwltool/cwlprov/provenance_constants.py index 7e0480e90..6a9c060ef 100644 --- a/cwltool/cwlprov/provenance_constants.py +++ b/cwltool/cwlprov/provenance_constants.py @@ -20,7 +20,7 @@ METADATA = "metadata" # sub-folders for data DATA = "data/input" -DATAX = "data" +# DATAX = "data" INPUT_DATA = "data/input" INTM_DATA = "data/intermediate" OUTPUT_DATA = "data/output" diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 271ed46fd..fcc911c92 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -32,7 +32,7 @@ from ..utils import CWLObjectType, JobsType, get_listing, posix_path, versionstring from ..workflow_job import WorkflowJob from . import provenance_constants -from .provenance_constants import ( +from .provenance_constants import ( # DATAX, ACCOUNT_UUID, CWLPROV, ENCODING, @@ -48,7 +48,7 @@ UUID, WF4EVER, WFDESC, - WFPROV, DATAX, + WFPROV, ) from .writablebagfile import create_job, write_bag_file # change this later @@ -305,7 +305,7 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st # TODO Input, intermediate or output file?... # if provenance_constants.DATA == 'data/input' if method == SHA1 and self.research_object.has_data_file( - provenance_constants.DATA, checksum # DATAX + provenance_constants.DATA, checksum # DATAX ): entity = self.document.entity("data:" + checksum) @@ -413,9 +413,9 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: # FIXME: .listing might not be populated yet - hopefully # a later call to this method will sort that is_empty = True - + # get loadlisting, and load the listing if not no_listing, recursively if deep_listing - ll = value.get("loadListing") + ll = value.get("loadListing") if ll and ll != "no_listing": get_listing(self.fsaccess, value, (ll == "deep_listing")) for entry in cast(MutableSequence[CWLObjectType], value.get("listing", [])): diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 34006f690..4fb83cf22 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -45,7 +45,7 @@ checksum_only, provenance_constants, ) -from .provenance_constants import ( +from .provenance_constants import ( # DATAX, ACCOUNT_UUID, CWLPROV_VERSION, ENCODING, @@ -62,7 +62,7 @@ USER_UUID, UUID, WORKFLOW, - Hasher, DATAX, + Hasher, ) @@ -504,21 +504,23 @@ def add_data_file( if self.no_data: checksum = checksum_only(from_fp) # Create rel_path - folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) # DATAX + folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) # DATAX path = os.path.join(folder, checksum) # Relative posix path rel_path = posix_path(os.path.relpath(path, self.folder)) elif self.no_input and provenance_constants.DATA == provenance_constants.INPUT_DATA: checksum = checksum_only(from_fp) # Create rel_path - folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) # DATAX + folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) # DATAX path = os.path.join(folder, checksum) # Relative posix path rel_path = posix_path(os.path.relpath(path, self.folder)) else: with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp: checksum = checksum_copy(from_fp, tmp) - folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) # DATAX + folder = os.path.join( + self.folder, provenance_constants.DATA, checksum[0:2] + ) # DATAX path = os.path.join(folder, checksum) if not os.path.isdir(folder): os.makedirs(folder) @@ -557,7 +559,6 @@ def add_data_file( self._content_types[rel_path] = content_type return rel_path - def _self_made( self, timestamp: Optional[datetime.datetime] = None ) -> Tuple[str, Dict[str, str]]: # createdOn, createdBy @@ -638,7 +639,7 @@ def _relativise_files( f"Only SHA1 CWL checksums are currently supported: {structure}" ) - if self.has_data_file(provenance_constants.DATA, checksum): # DATAX + if self.has_data_file(provenance_constants.DATA, checksum): # DATAX prefix = checksum[0:2] relative_path = PurePosixPath("data/input") / prefix / checksum From 97ad0c24037797b3ffd1542caecb56dc1e7fb64a Mon Sep 17 00:00:00 2001 From: Changlin Date: Tue, 25 Jun 2024 09:58:45 +0000 Subject: [PATCH 20/34] changed contents in provenance --- cwlref-runner/README | 2 +- cwltool/cwlprov/__init__.py | 15 ++++++--------- cwltool/cwlprov/provenance_constants.py | 3 ++- cwltool/cwlprov/provenance_profile.py | 17 +++++++++++------ 4 files changed, 20 insertions(+), 17 deletions(-) diff --git a/cwlref-runner/README b/cwlref-runner/README index 324751be2..bb1920fa1 100644 --- a/cwlref-runner/README +++ b/cwlref-runner/README @@ -1,4 +1,4 @@ -This an optional companion package to "cwltool" which provides provides an +This an optional companion package to "cwltool" which provides an additional entry point under the alias "cwl-runner", which is the implementation-agnostic name for the default CWL interpreter installed on a host. diff --git a/cwltool/cwlprov/__init__.py b/cwltool/cwlprov/__init__.py index fe91037a0..7a22f83af 100644 --- a/cwltool/cwlprov/__init__.py +++ b/cwltool/cwlprov/__init__.py @@ -6,7 +6,7 @@ import re import uuid from getpass import getuser -from typing import IO, Any, Dict, List, Optional, Tuple, TypedDict, Union +from typing import IO, Any, Callable, Dict, List, Optional, Tuple, TypedDict, Union from cwltool.cwlprov.provenance_constants import Hasher @@ -139,17 +139,16 @@ class AuthoredBy(TypedDict, total=False): def checksum_copy( src_file: IO[Any], dst_file: Optional[IO[Any]] = None, - hasher=Hasher, # type: Callable[[], hashlib._Hash] + hasher: Optional[str] = Hasher, buffersize: int = 1024 * 1024, ) -> str: """Compute checksums while copying a file.""" - # TODO: Use hashlib.new(Hasher_str) instead? if hasher: - checksum = hasher() + checksum = hashlib.new(hasher) else: from .provenance_constants import Hasher - checksum = Hasher() + checksum = hashlib.new(Hasher) contents = src_file.read(buffersize) if dst_file and hasattr(dst_file, "name") and hasattr(src_file, "name"): temp_location = os.path.join(os.path.dirname(dst_file.name), str(uuid.uuid4())) @@ -169,7 +168,7 @@ def checksum_copy( def checksum_only( src_file: IO[Any], dst_file: Optional[IO[Any]] = None, - hasher=Hasher, # type: Callable[[], hashlib._Hash] + hasher: Optional[str] = Hasher, buffersize: int = 1024 * 1024, ) -> str: """Calculate the checksum only, does not copy the data files.""" @@ -178,10 +177,8 @@ def checksum_only( "[Debug Checksum Only] Destination file should be None but it is %s", dst_file ) """Compute checksums while copying a file.""" - # TODO: Use hashlib.new(Hasher_str) instead? - checksum = hasher() + checksum = hashlib.new(hasher) contents = src_file.read(buffersize) - # TODO Could be a function for both checksum_only and checksum_copy? return content_processor(contents, src_file, dst_file, checksum, buffersize) diff --git a/cwltool/cwlprov/provenance_constants.py b/cwltool/cwlprov/provenance_constants.py index 6a9c060ef..b48e09618 100644 --- a/cwltool/cwlprov/provenance_constants.py +++ b/cwltool/cwlprov/provenance_constants.py @@ -49,10 +49,11 @@ # sha1, compatible with the File type's "checksum" field # e.g. "checksum" = "sha1$47a013e660d408619d894b20806b1d5086aab03b" # See ./cwltool/schemas/v1.0/Process.yml -Hasher = hashlib.sha1 SHA1 = "sha1" SHA256 = "sha256" SHA512 = "sha512" +# set the default hash function as SHA1 for hashlib.new +Hasher = SHA1 # TODO: Better identifiers for user, at least # these should be preserved in ~/.config/cwl for every execution diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index fcc911c92..7da979481 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -31,7 +31,7 @@ from ..stdfsaccess import StdFsAccess from ..utils import CWLObjectType, JobsType, get_listing, posix_path, versionstring from ..workflow_job import WorkflowJob -from . import provenance_constants +# from . import provenance_constants from .provenance_constants import ( # DATAX, ACCOUNT_UUID, CWLPROV, @@ -44,11 +44,16 @@ SCHEMA, SHA1, SHA256, + Hasher, TEXT_PLAIN, UUID, WF4EVER, WFDESC, WFPROV, + DATA, + OUTPUT_DATA, + INPUT_DATA, + INTM_DATA, ) from .writablebagfile import create_job, write_bag_file # change this later @@ -153,7 +158,7 @@ def host_provenance(document: ProvDocument) -> None: # https://tools.ietf.org/html/draft-thiemann-hash-urn-01 # TODO: Change to nih:sha-256; hashes # https://tools.ietf.org/html/rfc6920#section-7 - self.document.add_namespace("data", "urn:hash::sha1:") + self.document.add_namespace("data", f"urn:hash::{Hasher}:") # Also needed for docker images self.document.add_namespace(SHA256, "nih:sha-256;") @@ -303,12 +308,12 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st csum = cast(str, value["checksum"]) (method, checksum) = csum.split("$", 1) # TODO Input, intermediate or output file?... - # if provenance_constants.DATA == 'data/input' + # if DATA == 'data/input' if method == SHA1 and self.research_object.has_data_file( - provenance_constants.DATA, checksum # DATAX + DATA, checksum # DATAX ): entity = self.document.entity("data:" + checksum) - + if not entity and "location" in value: location = str(value["location"]) # If we made it here, we'll have to add it to the RO @@ -645,7 +650,7 @@ def generate_output_prov( ) -> None: """Call wasGeneratedBy() for each output, copy the files into the RO.""" # TODO: Change INPUT_DATA to OUTPUT_DATA? - provenance_constants.DATA = provenance_constants.OUTPUT_DATA + DATA = OUTPUT_DATA if isinstance(final_output, MutableSequence): for entry in final_output: From 7d6f35a0434bbb4436db8423e3b31c1f98b415a8 Mon Sep 17 00:00:00 2001 From: Changlin Date: Thu, 27 Jun 2024 22:37:30 +0000 Subject: [PATCH 21/34] MADE PROVENANCE_CONSTANTS CONSTANT AGAIN, ADDED SOME COMMENTS --- cwltool/argparser.py | 4 +- cwltool/cwlprov/__init__.py | 1 - cwltool/cwlprov/provenance_constants.py | 3 +- cwltool/cwlprov/provenance_profile.py | 40 ++++++++----- cwltool/cwlprov/ro.py | 80 +++++++++++-------------- cwltool/cwlprov/writablebagfile.py | 4 +- 6 files changed, 66 insertions(+), 66 deletions(-) diff --git a/cwltool/argparser.py b/cwltool/argparser.py index 72f999dd4..d59a68c01 100644 --- a/cwltool/argparser.py +++ b/cwltool/argparser.py @@ -292,7 +292,7 @@ def arg_parser() -> argparse.ArgumentParser: "--no-data", # Maybe change to no-input and no-intermediate to ignore those kind of files?... default=False, action="store_true", - help="Disables the storage of input and output data files", + help="Disables the storage of input and output data files in provenence folder", dest="no_data", ) @@ -301,7 +301,7 @@ def arg_parser() -> argparse.ArgumentParser: "--no-input", # Maybe change to no-input and no-intermediate to ignore those kind of files?... default=False, action="store_true", - help="Disables the storage of input data files", + help="Disables the storage of input data files in provenence folder", dest="no_input", ) diff --git a/cwltool/cwlprov/__init__.py b/cwltool/cwlprov/__init__.py index 7a22f83af..76f5e76a0 100644 --- a/cwltool/cwlprov/__init__.py +++ b/cwltool/cwlprov/__init__.py @@ -176,7 +176,6 @@ def checksum_only( _logger.error( "[Debug Checksum Only] Destination file should be None but it is %s", dst_file ) - """Compute checksums while copying a file.""" checksum = hashlib.new(hasher) contents = src_file.read(buffersize) return content_processor(contents, src_file, dst_file, checksum, buffersize) diff --git a/cwltool/cwlprov/provenance_constants.py b/cwltool/cwlprov/provenance_constants.py index b48e09618..4aefdf6af 100644 --- a/cwltool/cwlprov/provenance_constants.py +++ b/cwltool/cwlprov/provenance_constants.py @@ -19,8 +19,7 @@ # Research Object folders METADATA = "metadata" # sub-folders for data -DATA = "data/input" -# DATAX = "data" +DATA = "data" INPUT_DATA = "data/input" INTM_DATA = "data/intermediate" OUTPUT_DATA = "data/output" diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 7da979481..324036d5c 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -32,7 +32,7 @@ from ..utils import CWLObjectType, JobsType, get_listing, posix_path, versionstring from ..workflow_job import WorkflowJob # from . import provenance_constants -from .provenance_constants import ( # DATAX, +from .provenance_constants import ( ACCOUNT_UUID, CWLPROV, ENCODING, @@ -51,9 +51,8 @@ WFDESC, WFPROV, DATA, - OUTPUT_DATA, INPUT_DATA, - INTM_DATA, + OUTPUT_DATA, ) from .writablebagfile import create_job, write_bag_file # change this later @@ -117,6 +116,7 @@ def __init__( _logger.debug("[provenance] Creator Full name: %s", self.full_name) self.workflow_run_uuid = run_uuid or uuid.uuid4() self.workflow_run_uri = self.workflow_run_uuid.urn + self.current_data_source = INPUT_DATA # default to input data, now only INPUT_DATA and OUTPUT_DATA are possible values self.generate_prov_doc() def __str__(self) -> str: @@ -124,7 +124,15 @@ def __str__(self) -> str: return f"ProvenanceProfile <{self.workflow_run_uri}> in <{self.research_object}>" def generate_prov_doc(self) -> Tuple[str, ProvDocument]: - """Add basic namespaces.""" + """Generates a provenance document. + + This method adds basic namespaces to the provenance document and records host provenance. + It also adds information about the cwltool version, namespaces for various entities, + and creates agents, activities, and associations to represent the workflow execution. + + Returns: + A tuple containing the workflow run URI and the generated ProvDocument. + """ def host_provenance(document: ProvDocument) -> None: """Record host provenance.""" @@ -307,18 +315,17 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st if "checksum" in value: csum = cast(str, value["checksum"]) (method, checksum) = csum.split("$", 1) - # TODO Input, intermediate or output file?... - # if DATA == 'data/input' + # TODO intermediate file?... if method == SHA1 and self.research_object.has_data_file( - DATA, checksum # DATAX - ): + self.current_data_source, checksum + ): entity = self.document.entity("data:" + checksum) if not entity and "location" in value: location = str(value["location"]) # If we made it here, we'll have to add it to the RO with self.fsaccess.open(location, "rb") as fhandle: - relative_path = self.research_object.add_data_file(fhandle) + relative_path = self.research_object.add_data_file(fhandle, current_source = self.current_data_source) # FIXME: This naively relies on add_data_file setting hash as filename checksum = PurePath(relative_path).name entity = self.document.entity("data:" + checksum, {PROV_TYPE: WFPROV["Artifact"]}) @@ -419,8 +426,8 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: # a later call to this method will sort that is_empty = True - # get loadlisting, and load the listing if not no_listing, recursively if deep_listing - ll = value.get("loadListing") + # get loadlisting, and populate the listing of value if not no_listing, recursively if deep_listing + ll = value.get("loadListing") if ll and ll != "no_listing": get_listing(self.fsaccess, value, (ll == "deep_listing")) for entry in cast(MutableSequence[CWLObjectType], value.get("listing", [])): @@ -485,7 +492,7 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: def declare_string(self, value: str) -> Tuple[ProvEntity, str]: """Save as string in UTF-8.""" byte_s = BytesIO(str(value).encode(ENCODING)) - data_file = self.research_object.add_data_file(byte_s, content_type=TEXT_PLAIN) + data_file = self.research_object.add_data_file(byte_s, current_source = self.current_data_source, content_type=TEXT_PLAIN) checksum = PurePosixPath(data_file).name # FIXME: Don't naively assume add_data_file uses hash in filename! data_id = f"data:{PurePosixPath(data_file).stem}" @@ -518,7 +525,7 @@ def declare_artefact(self, value: Any) -> ProvEntity: if isinstance(value, bytes): # If we got here then we must be in Python 3 byte_s = BytesIO(value) - data_file = self.research_object.add_data_file(byte_s) + data_file = self.research_object.add_data_file(byte_s, current_source = self.current_data_source) # FIXME: Don't naively assume add_data_file uses hash in filename! data_id = f"data:{PurePosixPath(data_file).stem}" return self.document.entity( @@ -649,8 +656,9 @@ def generate_output_prov( name: Optional[str], ) -> None: """Call wasGeneratedBy() for each output, copy the files into the RO.""" - # TODO: Change INPUT_DATA to OUTPUT_DATA? - DATA = OUTPUT_DATA + # To save output data in ro.py add_data_file() method, use a var current_data_source to keep track of whether it's input or output (maybe intermediate in the future) data + # it is later injected to add_data_file() method to save the data in the correct folder, thus avoid changing the provenance_constants DATA + self.current_data_source = OUTPUT_DATA if isinstance(final_output, MutableSequence): for entry in final_output: @@ -677,6 +685,7 @@ def generate_output_prov( self.document.wasGeneratedBy( entity, process_run_id, timestamp, None, {"prov:role": role} ) + # return current_data_source def prospective_prov(self, job: JobsType) -> None: """Create prospective prov recording as wfdesc prov:Plan.""" @@ -750,6 +759,7 @@ def finalize_prov_profile(self, name: Optional[str]) -> List[QualifiedName]: # TODO: Also support other profiles than CWLProv, e.g. ProvOne # list of prov identifiers of provenance files + # prov_ids are file names prepared for provenance/RO files in metadata/provenance for each sub-workflow of main workflow prov_ids = [] # https://www.w3.org/TR/prov-xml/ diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 6b3b1778b..db064d134 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -45,7 +45,7 @@ checksum_only, provenance_constants, ) -from .provenance_constants import ( # DATAX, +from .provenance_constants import ( ACCOUNT_UUID, CWLPROV_VERSION, ENCODING, @@ -63,6 +63,9 @@ UUID, WORKFLOW, Hasher, + INPUT_DATA, + INTM_DATA, # NOT USED + OUTPUT_DATA, ) @@ -102,8 +105,6 @@ def __init__( self.no_data = no_data self.no_input = no_input - # TODO Fix...? Set the INPUT_DATA to default for input - # modify_data("data/inputs") self._initialize() _logger.debug("[provenance] Temporary research object: %s", self.folder) @@ -124,9 +125,9 @@ def _initialize(self) -> None: """Initialize the bagit folder structure.""" for research_obj_folder in ( METADATA, - provenance_constants.INPUT_DATA, - provenance_constants.INTM_DATA, - provenance_constants.OUTPUT_DATA, + INPUT_DATA, + INTM_DATA, # NOT POPULATED + OUTPUT_DATA, WORKFLOW, SNAPSHOT, PROVENANCE, @@ -198,23 +199,14 @@ def add_tagfile(self, path: str, timestamp: Optional[datetime.datetime] = None) # adding checksums after closing. # Below probably OK for now as metadata files # are not too large..? - # x = provenance_constants.DATA - if self.no_input and provenance_constants.DATA == "data/input": - _logger.debug("NO INPUT DATA TO BE CAPTURED!!!") - - checksums[SHA1] = checksum_only(tag_file, hasher=hashlib.sha1) - tag_file.seek(0) - checksums[SHA256] = checksum_only(tag_file, hasher=hashlib.sha256) - tag_file.seek(0) - checksums[SHA512] = checksum_only(tag_file, hasher=hashlib.sha512) - else: - checksums[SHA1] = checksum_copy(tag_file, hasher=hashlib.sha1) - tag_file.seek(0) - checksums[SHA256] = checksum_copy(tag_file, hasher=hashlib.sha256) + checksums[SHA1] = checksum_copy(tag_file, hasher=hashlib.sha1) + + tag_file.seek(0) + checksums[SHA256] = checksum_copy(tag_file, hasher=hashlib.sha256) - tag_file.seek(0) - checksums[SHA512] = checksum_copy(tag_file, hasher=hashlib.sha512) + tag_file.seek(0) + checksums[SHA512] = checksum_copy(tag_file, hasher=hashlib.sha512) rel_path = posix_path(os.path.relpath(path, self.folder)) self.tagfiles.add(rel_path) @@ -476,7 +468,7 @@ def generate_snapshot(self, prov_dep: CWLObjectType) -> None: else: shutil.copy(filepath, path) timestamp = datetime.datetime.fromtimestamp(os.path.getmtime(filepath)) - self.add_tagfile(path, timestamp) + self.add_tagfile(path, timestamp) # add snapshots as tag files to the RO except PermissionError: pass # FIXME: avoids duplicate snapshotting; need better solution elif key in ("secondaryFiles", "listing"): @@ -495,48 +487,44 @@ def has_data_file(self, location: str, sha1hash: str) -> bool: def add_data_file( self, from_fp: IO[Any], + current_source: str = None, # source/destination of the incoming file, e.g. "data/input" or "data/output" timestamp: Optional[datetime.datetime] = None, content_type: Optional[str] = None, ) -> str: - """Copy intermediate? inputs to data/ folder.""" - # provenance_constants.DATA = "data/intermediate" # Change to that ??? - # TODO: This also copies the outputs?... - # TODO Skip if no-input or no-data is used + """Copy data files to data/ folder.""" + # This also copies the outputs via declare_artefacts -> generate_output_prov + # Skip certain files if no-input or no-data is used self.self_check() tmp_dir, tmp_prefix = os.path.split(self.temp_prefix) if self.no_data: checksum = checksum_only(from_fp) # Create rel_path - folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) # DATAX - path = os.path.join(folder, checksum) - # Relative posix path - rel_path = posix_path(os.path.relpath(path, self.folder)) - elif self.no_input and provenance_constants.DATA == provenance_constants.INPUT_DATA: - checksum = checksum_only(from_fp) - # Create rel_path - folder = os.path.join(self.folder, provenance_constants.DATA, checksum[0:2]) # DATAX + folder = os.path.join( + self.folder, current_source, checksum[0:2] + ) path = os.path.join(folder, checksum) # Relative posix path rel_path = posix_path(os.path.relpath(path, self.folder)) else: + # calculate checksum and copy file to a tmp location with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp: checksum = checksum_copy(from_fp, tmp) folder = os.path.join( - self.folder, provenance_constants.DATA, checksum[0:2] - ) # DATAX + self.folder, current_source, checksum[0:2] + ) path = os.path.join(folder, checksum) if not os.path.isdir(folder): os.makedirs(folder) # Only rename when neither no data and no input is used os.rename(tmp.name, path) - _logger.debug("Renaming %s to %s", tmp.name, path) + _logger.debug("Renaming %s to %s", tmp.name, path) # path is still a temp dir but in "data/input/checksum last 2 digit/checksum" # Relative posix path rel_path = posix_path(os.path.relpath(path, self.folder)) # Register in bagit checksum if Hasher == hashlib.sha1: - self._add_to_bagit(rel_path, sha1=checksum) + self._add_to_bagit(rel_path, sha1=checksum) # that is actually saving the file to the prov RO folder else: _logger.warning( "[provenance] Unknown hash method %s for bagit manifest", Hasher @@ -573,7 +561,7 @@ def _self_made( ) def add_to_manifest(self, rel_path: str, checksums: Dict[str, str]) -> None: - """Add files to the research object manifest.""" + """Add files to the research object manifest. Data files are added to manifest regardless of the state of no_data/no_input flags""" self.self_check() if PurePosixPath(rel_path).is_absolute(): raise ValueError(f"rel_path must be relative: {rel_path}") @@ -598,10 +586,13 @@ def add_to_manifest(self, rel_path: str, checksums: Dict[str, str]) -> None: checksum_file.write(line) def _add_to_bagit(self, rel_path: str, **checksums: str) -> None: - """Compute file size and checksums and adds to bagit manifest.""" + """ + Compute data file size and checksums and adds to bagit manifest. + NOTE: THIS IS WHERE DATAFILE COPYING REALLY HAPPENS WITH checksum_copy + """ if PurePosixPath(rel_path).is_absolute(): raise ValueError(f"rel_path must be relative: {rel_path}") - lpath = os.path.join(self.folder, local_path(rel_path)) + lpath = os.path.join(self.folder, local_path(rel_path)) if not os.path.exists(lpath): raise OSError(f"File {rel_path} does not exist within RO: {lpath}") @@ -614,8 +605,9 @@ def _add_to_bagit(self, rel_path: str, **checksums: str) -> None: # ensure we always have sha1 checksums = dict(checksums) with open(lpath, "rb") as file_path: - # FIXME: Need sha-256 / sha-512 as well for Research Object BagIt profile? - if self.no_data or self.no_input: + # FIXME: Need sha-256 / sha-512 as well for Research Object BagIt profile? maybe slowing down the process a lot. + if self.no_input and os.path.commonprefix( + [provenance_constants.INPUT_DATA, lpath]) == provenance_constants.INPUT_DATA: checksums[SHA1] = checksum_only(file_path, hasher=hashlib.sha1) else: checksums[SHA1] = checksum_copy(file_path, hasher=hashlib.sha1) @@ -643,7 +635,7 @@ def _relativise_files( f"Only SHA1 CWL checksums are currently supported: {structure}" ) - if self.has_data_file(provenance_constants.DATA, checksum): # DATAX + if self.has_data_file(provenance_constants.INPUT_DATA, checksum): prefix = checksum[0:2] relative_path = PurePosixPath("data/input") / prefix / checksum diff --git a/cwltool/cwlprov/writablebagfile.py b/cwltool/cwlprov/writablebagfile.py index 8c1f9d7e2..38ef1f7bc 100644 --- a/cwltool/cwlprov/writablebagfile.py +++ b/cwltool/cwlprov/writablebagfile.py @@ -55,14 +55,14 @@ def __init__(self, research_object: "ResearchObject", rel_path: str) -> None: def write(self, b: Any) -> int: """Write some content to the Bag.""" real_b = b if isinstance(b, (bytes, mmap, array)) else b.encode("utf-8") - total = 0 + total = 0 # to record the total bytes written length = len(real_b) while total < length: ret = super().write(real_b) if ret: total += ret for val in self.hashes.values(): - val.update(real_b) + val.update(real_b) # update hash with the written content return total def close(self) -> None: From d052895153b6df12735a1cd8d9d5aa25b98657e5 Mon Sep 17 00:00:00 2001 From: Changlin Date: Thu, 27 Jun 2024 23:49:41 +0000 Subject: [PATCH 22/34] Fix hasher param type for checksum_copy, improve linting: flake8, pydocstyle --- cwltool/cwlprov/__init__.py | 6 +- cwltool/cwlprov/provenance_constants.py | 1 - cwltool/cwlprov/provenance_profile.py | 101 +++++++++++++++++------- cwltool/cwlprov/ro.py | 93 ++++++++++++++-------- cwltool/cwlprov/writablebagfile.py | 12 ++- 5 files changed, 142 insertions(+), 71 deletions(-) diff --git a/cwltool/cwlprov/__init__.py b/cwltool/cwlprov/__init__.py index 76f5e76a0..af7ca99c1 100644 --- a/cwltool/cwlprov/__init__.py +++ b/cwltool/cwlprov/__init__.py @@ -6,7 +6,7 @@ import re import uuid from getpass import getuser -from typing import IO, Any, Callable, Dict, List, Optional, Tuple, TypedDict, Union +from typing import IO, Any, Dict, List, Optional, Tuple, TypedDict, Union from cwltool.cwlprov.provenance_constants import Hasher @@ -139,7 +139,7 @@ class AuthoredBy(TypedDict, total=False): def checksum_copy( src_file: IO[Any], dst_file: Optional[IO[Any]] = None, - hasher: Optional[str] = Hasher, + hasher: Optional[str] = Hasher, buffersize: int = 1024 * 1024, ) -> str: """Compute checksums while copying a file.""" @@ -168,7 +168,7 @@ def checksum_copy( def checksum_only( src_file: IO[Any], dst_file: Optional[IO[Any]] = None, - hasher: Optional[str] = Hasher, + hasher: Optional[str] = Hasher, buffersize: int = 1024 * 1024, ) -> str: """Calculate the checksum only, does not copy the data files.""" diff --git a/cwltool/cwlprov/provenance_constants.py b/cwltool/cwlprov/provenance_constants.py index 4aefdf6af..bce87337a 100644 --- a/cwltool/cwlprov/provenance_constants.py +++ b/cwltool/cwlprov/provenance_constants.py @@ -1,4 +1,3 @@ -import hashlib import os import uuid diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 324036d5c..f5ca8e32d 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -31,8 +31,9 @@ from ..stdfsaccess import StdFsAccess from ..utils import CWLObjectType, JobsType, get_listing, posix_path, versionstring from ..workflow_job import WorkflowJob + # from . import provenance_constants -from .provenance_constants import ( +from .provenance_constants import ( ACCOUNT_UUID, CWLPROV, ENCODING, @@ -50,7 +51,6 @@ WF4EVER, WFDESC, WFPROV, - DATA, INPUT_DATA, OUTPUT_DATA, ) @@ -60,7 +60,9 @@ from .ro import ResearchObject -def copy_job_order(job: Union[Process, JobsType], job_order_object: CWLObjectType) -> CWLObjectType: +def copy_job_order( + job: Union[Process, JobsType], job_order_object: CWLObjectType +) -> CWLObjectType: """Create copy of job object for provenance.""" if not isinstance(job, WorkflowJob): # direct command line tool execution @@ -116,15 +118,18 @@ def __init__( _logger.debug("[provenance] Creator Full name: %s", self.full_name) self.workflow_run_uuid = run_uuid or uuid.uuid4() self.workflow_run_uri = self.workflow_run_uuid.urn - self.current_data_source = INPUT_DATA # default to input data, now only INPUT_DATA and OUTPUT_DATA are possible values + # default to input data, now only INPUT_DATA and OUTPUT_DATA are possible values + self.current_data_source = INPUT_DATA self.generate_prov_doc() def __str__(self) -> str: """Represent this Provenvance profile as a string.""" - return f"ProvenanceProfile <{self.workflow_run_uri}> in <{self.research_object}>" + return ( + f"ProvenanceProfile <{self.workflow_run_uri}> in <{self.research_object}>" + ) def generate_prov_doc(self) -> Tuple[str, ProvDocument]: - """Generates a provenance document. + """Generate a provenance document. This method adds basic namespaces to the provenance document and records host provenance. It also adds information about the cwltool version, namespaces for various entities, @@ -182,7 +187,9 @@ def host_provenance(document: ProvDocument) -> None: ) ro_identifier_workflow = self.research_object.base_uri + "workflow/packed.cwl#" self.wf_ns = self.document.add_namespace("wf", ro_identifier_workflow) - ro_identifier_input = self.research_object.base_uri + "workflow/primary-job.json#" + ro_identifier_input = ( + self.research_object.base_uri + "workflow/primary-job.json#" + ) self.document.add_namespace("input", ro_identifier_input) # More info about the account (e.g. username, fullname) @@ -233,7 +240,9 @@ def host_provenance(document: ProvDocument) -> None: ) # association between SoftwareAgent and WorkflowRun main_workflow = "wf:main" - self.document.wasAssociatedWith(self.workflow_run_uri, self.engine_uuid, main_workflow) + self.document.wasAssociatedWith( + self.workflow_run_uri, self.engine_uuid, main_workflow + ) self.document.wasStartedBy( self.workflow_run_uri, None, self.engine_uuid, datetime.datetime.now() ) @@ -292,7 +301,9 @@ def start_process( self.document.wasAssociatedWith( process_run_id, self.engine_uuid, str("wf:main/" + process_name) ) - self.document.wasStartedBy(process_run_id, None, self.workflow_run_uri, when, None, None) + self.document.wasStartedBy( + process_run_id, None, self.workflow_run_uri, when, None, None + ) return process_run_id def record_process_end( @@ -317,18 +328,22 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st (method, checksum) = csum.split("$", 1) # TODO intermediate file?... if method == SHA1 and self.research_object.has_data_file( - self.current_data_source, checksum - ): + self.current_data_source, checksum + ): entity = self.document.entity("data:" + checksum) - + if not entity and "location" in value: location = str(value["location"]) # If we made it here, we'll have to add it to the RO with self.fsaccess.open(location, "rb") as fhandle: - relative_path = self.research_object.add_data_file(fhandle, current_source = self.current_data_source) + relative_path = self.research_object.add_data_file( + fhandle, current_source=self.current_data_source + ) # FIXME: This naively relies on add_data_file setting hash as filename checksum = PurePath(relative_path).name - entity = self.document.entity("data:" + checksum, {PROV_TYPE: WFPROV["Artifact"]}) + entity = self.document.entity( + "data:" + checksum, {PROV_TYPE: WFPROV["Artifact"]} + ) if "checksum" not in value: value["checksum"] = f"{SHA1}${checksum}" @@ -338,7 +353,9 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st # By here one of them should have worked! if not entity or not checksum: - raise ValueError("class:File but missing checksum/location/content: %r" % value) + raise ValueError( + "class:File but missing checksum/location/content: %r" % value + ) # Track filename and extension, this is generally useful only for # secondaryFiles. Note that multiple uses of a file might thus record @@ -352,15 +369,23 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st ) if "basename" in value: - file_entity.add_attributes({CWLPROV["basename"]: cast(str, value["basename"])}) + file_entity.add_attributes( + {CWLPROV["basename"]: cast(str, value["basename"])} + ) if "nameroot" in value: - file_entity.add_attributes({CWLPROV["nameroot"]: cast(str, value["nameroot"])}) + file_entity.add_attributes( + {CWLPROV["nameroot"]: cast(str, value["nameroot"])} + ) if "nameext" in value: - file_entity.add_attributes({CWLPROV["nameext"]: cast(str, value["nameext"])}) + file_entity.add_attributes( + {CWLPROV["nameext"]: cast(str, value["nameext"])} + ) self.document.specializationOf(file_entity, entity) # Check for secondaries - for sec in cast(MutableSequence[CWLObjectType], value.get("secondaryFiles", [])): + for sec in cast( + MutableSequence[CWLObjectType], value.get("secondaryFiles", []) + ): # TODO: Record these in a specializationOf entity with UUID? if sec["class"] == "File": (sec_entity, _, _) = self.declare_file(sec) @@ -427,7 +452,7 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: is_empty = True # get loadlisting, and populate the listing of value if not no_listing, recursively if deep_listing - ll = value.get("loadListing") + ll = value.get("loadListing") if ll and ll != "no_listing": get_listing(self.fsaccess, value, (ll == "deep_listing")) for entry in cast(MutableSequence[CWLObjectType], value.get("listing", [])): @@ -480,7 +505,9 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: ore_doc_path = str(PurePosixPath(METADATA, ore_doc_fn)) with write_bag_file(self.research_object, ore_doc_path) as provenance_file: ore_doc.serialize(provenance_file, format="rdf", rdf_format="turtle") - self.research_object.add_annotation(dir_id, [ore_doc_fn], ORE["isDescribedBy"].uri) + self.research_object.add_annotation( + dir_id, [ore_doc_fn], ORE["isDescribedBy"].uri + ) if is_empty: # Empty directory @@ -492,7 +519,9 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: def declare_string(self, value: str) -> Tuple[ProvEntity, str]: """Save as string in UTF-8.""" byte_s = BytesIO(str(value).encode(ENCODING)) - data_file = self.research_object.add_data_file(byte_s, current_source = self.current_data_source, content_type=TEXT_PLAIN) + data_file = self.research_object.add_data_file( + byte_s, current_source=self.current_data_source, content_type=TEXT_PLAIN + ) checksum = PurePosixPath(data_file).name # FIXME: Don't naively assume add_data_file uses hash in filename! data_id = f"data:{PurePosixPath(data_file).stem}" @@ -525,7 +554,9 @@ def declare_artefact(self, value: Any) -> ProvEntity: if isinstance(value, bytes): # If we got here then we must be in Python 3 byte_s = BytesIO(value) - data_file = self.research_object.add_data_file(byte_s, current_source = self.current_data_source) + data_file = self.research_object.add_data_file( + byte_s, current_source=self.current_data_source + ) # FIXME: Don't naively assume add_data_file uses hash in filename! data_id = f"data:{PurePosixPath(data_file).stem}" return self.document.entity( @@ -578,7 +609,9 @@ def declare_artefact(self, value: Any) -> ProvEntity: # https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition # as prov.py do not easily allow PROV-N extensions m_entity.add_asserted_type(PROV["KeyEntityPair"]) - m_entity.add_attributes({PROV["pairKey"]: str(key), PROV["pairEntity"]: v_ent}) + m_entity.add_attributes( + {PROV["pairKey"]: str(key), PROV["pairEntity"]: v_ent} + ) coll_attribs.append((PROV["hadDictionaryMember"], m_entity)) coll.add_attributes(coll_attribs) self.research_object.add_uri(coll.identifier.uri) @@ -726,7 +759,9 @@ def prospective_prov(self, job: JobsType) -> None: ) # TODO: Declare roles/parameters as well - def activity_has_provenance(self, activity: str, prov_ids: Sequence[Identifier]) -> None: + def activity_has_provenance( + self, activity: str, prov_ids: Sequence[Identifier] + ) -> None: """Add http://www.w3.org/TR/prov-aq/ relations to nested PROV files.""" # NOTE: The below will only work if the corresponding metadata/provenance arcp URI # is a pre-registered namespace in the PROV Document @@ -768,12 +803,16 @@ def finalize_prov_profile(self, name: Optional[str]) -> List[QualifiedName]: prov_ids.append(self.provenance_ns[filename + ".xml"]) # https://www.w3.org/TR/prov-n/ - with write_bag_file(self.research_object, basename + ".provn") as provenance_file: + with write_bag_file( + self.research_object, basename + ".provn" + ) as provenance_file: self.document.serialize(provenance_file, format="provn", indent=2) prov_ids.append(self.provenance_ns[filename + ".provn"]) # https://www.w3.org/Submission/prov-json/ - with write_bag_file(self.research_object, basename + ".json") as provenance_file: + with write_bag_file( + self.research_object, basename + ".json" + ) as provenance_file: self.document.serialize(provenance_file, format="json", indent=2) prov_ids.append(self.provenance_ns[filename + ".json"]) @@ -787,14 +826,18 @@ def finalize_prov_profile(self, name: Optional[str]) -> List[QualifiedName]: # https://www.w3.org/TR/n-triples/ with write_bag_file(self.research_object, basename + ".nt") as provenance_file: - self.document.serialize(provenance_file, format="rdf", rdf_format="ntriples") + self.document.serialize( + provenance_file, format="rdf", rdf_format="ntriples" + ) prov_ids.append(self.provenance_ns[filename + ".nt"]) # https://www.w3.org/TR/json-ld/ # TODO: Use a nice JSON-LD context # see also https://eprints.soton.ac.uk/395985/ # 404 Not Found on https://provenance.ecs.soton.ac.uk/prov.jsonld :( - with write_bag_file(self.research_object, basename + ".jsonld") as provenance_file: + with write_bag_file( + self.research_object, basename + ".jsonld" + ) as provenance_file: self.document.serialize(provenance_file, format="rdf", rdf_format="json-ld") prov_ids.append(self.provenance_ns[filename + ".jsonld"]) diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index db064d134..b0e39b994 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -45,7 +45,7 @@ checksum_only, provenance_constants, ) -from .provenance_constants import ( +from .provenance_constants import ( ACCOUNT_UUID, CWLPROV_VERSION, ENCODING, @@ -64,7 +64,7 @@ WORKFLOW, Hasher, INPUT_DATA, - INTM_DATA, # NOT USED + INTM_DATA, # NOT USED OUTPUT_DATA, ) @@ -105,7 +105,6 @@ def __init__( self.no_data = no_data self.no_input = no_input - self._initialize() _logger.debug("[provenance] Temporary research object: %s", self.folder) @@ -126,7 +125,7 @@ def _initialize(self) -> None: for research_obj_folder in ( METADATA, INPUT_DATA, - INTM_DATA, # NOT POPULATED + INTM_DATA, # NOT POPULATED OUTPUT_DATA, WORKFLOW, SNAPSHOT, @@ -185,7 +184,9 @@ def user_provenance(self, document: ProvDocument) -> None: # get their name wrong!) document.actedOnBehalfOf(account, user) - def add_tagfile(self, path: str, timestamp: Optional[datetime.datetime] = None) -> None: + def add_tagfile( + self, path: str, timestamp: Optional[datetime.datetime] = None + ) -> None: """Add tag files to our research object.""" self.self_check() checksums = {} @@ -200,13 +201,13 @@ def add_tagfile(self, path: str, timestamp: Optional[datetime.datetime] = None) # Below probably OK for now as metadata files # are not too large..? - checksums[SHA1] = checksum_copy(tag_file, hasher=hashlib.sha1) + checksums[SHA1] = checksum_copy(tag_file, hasher=SHA1) tag_file.seek(0) - checksums[SHA256] = checksum_copy(tag_file, hasher=hashlib.sha256) + checksums[SHA256] = checksum_copy(tag_file, hasher=SHA256) tag_file.seek(0) - checksums[SHA512] = checksum_copy(tag_file, hasher=hashlib.sha512) + checksums[SHA512] = checksum_copy(tag_file, hasher=SHA512) rel_path = posix_path(os.path.relpath(path, self.folder)) self.tagfiles.add(rel_path) @@ -262,11 +263,16 @@ def guess_mediatype( extension = None mediatype: Optional[str] = media_types.get(extension, None) - conformsTo: Optional[Union[str, List[str]]] = conforms_to.get(extension, None) + conformsTo: Optional[Union[str, List[str]]] = conforms_to.get( + extension, None + ) # TODO: Open CWL file to read its declared "cwlVersion", e.g. # cwlVersion = "v1.0" - if rel_path.startswith(posix_path(PROVENANCE)) and extension in prov_conforms_to: + if ( + rel_path.startswith(posix_path(PROVENANCE)) + and extension in prov_conforms_to + ): if ".cwlprov" in rel_path: # Our own! conformsTo = [ @@ -321,7 +327,9 @@ def guess_mediatype( for path in self.tagfiles: if not ( - path.startswith(METADATA) or path.startswith(WORKFLOW) or path.startswith(SNAPSHOT) + path.startswith(METADATA) + or path.startswith(WORKFLOW) + or path.startswith(SNAPSHOT) ): # probably a bagit file continue @@ -353,7 +361,9 @@ def guess_mediatype( aggregates.extend(self._external_aggregates) return aggregates - def add_uri(self, uri: str, timestamp: Optional[datetime.datetime] = None) -> Aggregate: + def add_uri( + self, uri: str, timestamp: Optional[datetime.datetime] = None + ) -> Aggregate: self.self_check() aggr: Aggregate = {"uri": uri} aggr["createdOn"], aggr["createdBy"] = self._self_made(timestamp=timestamp) @@ -467,8 +477,12 @@ def generate_snapshot(self, prov_dep: CWLObjectType) -> None: shutil.copytree(filepath, path) else: shutil.copy(filepath, path) - timestamp = datetime.datetime.fromtimestamp(os.path.getmtime(filepath)) - self.add_tagfile(path, timestamp) # add snapshots as tag files to the RO + timestamp = datetime.datetime.fromtimestamp( + os.path.getmtime(filepath) + ) + self.add_tagfile( + path, timestamp + ) # add snapshots as tag files to the RO except PermissionError: pass # FIXME: avoids duplicate snapshotting; need better solution elif key in ("secondaryFiles", "listing"): @@ -487,7 +501,7 @@ def has_data_file(self, location: str, sha1hash: str) -> bool: def add_data_file( self, from_fp: IO[Any], - current_source: str = None, # source/destination of the incoming file, e.g. "data/input" or "data/output" + current_source: str = None, # source/destination of the incoming file, e.g. "data/input" or "data/output" timestamp: Optional[datetime.datetime] = None, content_type: Optional[str] = None, ) -> str: @@ -499,32 +513,34 @@ def add_data_file( if self.no_data: checksum = checksum_only(from_fp) # Create rel_path - folder = os.path.join( - self.folder, current_source, checksum[0:2] - ) + folder = os.path.join(self.folder, current_source, checksum[0:2]) path = os.path.join(folder, checksum) # Relative posix path rel_path = posix_path(os.path.relpath(path, self.folder)) else: - # calculate checksum and copy file to a tmp location - with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp: + # calculate checksum and copy file to a tmp location + with tempfile.NamedTemporaryFile( + prefix=tmp_prefix, dir=tmp_dir, delete=False + ) as tmp: checksum = checksum_copy(from_fp, tmp) - folder = os.path.join( - self.folder, current_source, checksum[0:2] - ) + folder = os.path.join(self.folder, current_source, checksum[0:2]) path = os.path.join(folder, checksum) if not os.path.isdir(folder): os.makedirs(folder) # Only rename when neither no data and no input is used os.rename(tmp.name, path) - _logger.debug("Renaming %s to %s", tmp.name, path) # path is still a temp dir but in "data/input/checksum last 2 digit/checksum" + _logger.debug( + "Renaming %s to %s", tmp.name, path + ) # path is still a temp dir but in "data/input/checksum last 2 digit/checksum" # Relative posix path rel_path = posix_path(os.path.relpath(path, self.folder)) # Register in bagit checksum if Hasher == hashlib.sha1: - self._add_to_bagit(rel_path, sha1=checksum) # that is actually saving the file to the prov RO folder + self._add_to_bagit( + rel_path, sha1=checksum + ) # that is actually saving the file to the prov RO folder else: _logger.warning( "[provenance] Unknown hash method %s for bagit manifest", Hasher @@ -561,7 +577,7 @@ def _self_made( ) def add_to_manifest(self, rel_path: str, checksums: Dict[str, str]) -> None: - """Add files to the research object manifest. Data files are added to manifest regardless of the state of no_data/no_input flags""" + """Add files to the research object manifest. Data files are added to manifest regardless of the state of no_data/no_input flag.""" self.self_check() if PurePosixPath(rel_path).is_absolute(): raise ValueError(f"rel_path must be relative: {rel_path}") @@ -580,19 +596,23 @@ def add_to_manifest(self, rel_path: str, checksums: Dict[str, str]) -> None: # existence in bagged_size above manifestpath = os.path.join(self.folder, f"{manifest}-{method.lower()}.txt") # encoding: match Tag-File-Character-Encoding: UTF-8 - with open(manifestpath, "a", encoding=ENCODING, newline="\n") as checksum_file: + with open( + manifestpath, "a", encoding=ENCODING, newline="\n" + ) as checksum_file: line = f"{hash_value} {rel_path}\n" _logger.debug("[provenance] Added to %s: %s", manifestpath, line) checksum_file.write(line) def _add_to_bagit(self, rel_path: str, **checksums: str) -> None: + """ Compute data file size and checksums and adds to bagit manifest. NOTE: THIS IS WHERE DATAFILE COPYING REALLY HAPPENS WITH checksum_copy """ + if PurePosixPath(rel_path).is_absolute(): raise ValueError(f"rel_path must be relative: {rel_path}") - lpath = os.path.join(self.folder, local_path(rel_path)) + lpath = os.path.join(self.folder, local_path(rel_path)) if not os.path.exists(lpath): raise OSError(f"File {rel_path} does not exist within RO: {lpath}") @@ -606,11 +626,14 @@ def _add_to_bagit(self, rel_path: str, **checksums: str) -> None: checksums = dict(checksums) with open(lpath, "rb") as file_path: # FIXME: Need sha-256 / sha-512 as well for Research Object BagIt profile? maybe slowing down the process a lot. - if self.no_input and os.path.commonprefix( - [provenance_constants.INPUT_DATA, lpath]) == provenance_constants.INPUT_DATA: - checksums[SHA1] = checksum_only(file_path, hasher=hashlib.sha1) + if ( + self.no_input + and os.path.commonprefix([provenance_constants.INPUT_DATA, lpath]) + == provenance_constants.INPUT_DATA + ): + checksums[SHA1] = checksum_only(file_path, hasher=SHA1) else: - checksums[SHA1] = checksum_copy(file_path, hasher=hashlib.sha1) + checksums[SHA1] = checksum_copy(file_path, hasher=SHA1) self.add_to_manifest(rel_path, checksums) @@ -635,7 +658,7 @@ def _relativise_files( f"Only SHA1 CWL checksums are currently supported: {structure}" ) - if self.has_data_file(provenance_constants.INPUT_DATA, checksum): + if self.has_data_file(provenance_constants.INPUT_DATA, checksum): prefix = checksum[0:2] relative_path = PurePosixPath("data/input") / prefix / checksum @@ -647,7 +670,9 @@ def _relativise_files( structure["basename"], structure["location"], ) - with self.fsaccess.open(cast(str, structure["location"]), "rb") as fp: + with self.fsaccess.open( + cast(str, structure["location"]), "rb" + ) as fp: relative_path = self.add_data_file(fp) checksum = PurePosixPath(relative_path).name structure["checksum"] = f"{SHA1}${checksum}" diff --git a/cwltool/cwlprov/writablebagfile.py b/cwltool/cwlprov/writablebagfile.py index 38ef1f7bc..e0ca4f76b 100644 --- a/cwltool/cwlprov/writablebagfile.py +++ b/cwltool/cwlprov/writablebagfile.py @@ -46,7 +46,9 @@ def __init__(self, research_object: "ResearchObject", rel_path: str) -> None: SHA512: hashlib.sha512(), } # Open file in Research Object folder - path = os.path.abspath(os.path.join(research_object.folder, local_path(rel_path))) + path = os.path.abspath( + os.path.join(research_object.folder, local_path(rel_path)) + ) if not path.startswith(os.path.abspath(research_object.folder)): raise ValueError("Path is outside Research Object: %s" % path) _logger.debug("[provenance] Creating WritableBagFile at %s.", path) @@ -55,14 +57,14 @@ def __init__(self, research_object: "ResearchObject", rel_path: str) -> None: def write(self, b: Any) -> int: """Write some content to the Bag.""" real_b = b if isinstance(b, (bytes, mmap, array)) else b.encode("utf-8") - total = 0 # to record the total bytes written + total = 0 # to record the total bytes written length = len(real_b) while total < length: ret = super().write(real_b) if ret: total += ret for val in self.hashes.values(): - val.update(real_b) # update hash with the written content + val.update(real_b) # update hash with the written content return total def close(self) -> None: @@ -238,7 +240,9 @@ def packed_workflow(research_object: "ResearchObject", packed: str) -> None: def create_job( - research_object: "ResearchObject", builder_job: CWLObjectType, is_output: bool = False + research_object: "ResearchObject", + builder_job: CWLObjectType, + is_output: bool = False, ) -> CWLObjectType: # TODO customise the file """Generate the new job object with RO specific relative paths.""" From 61024ffc2be98e2c07a52bbfe507957a5ac909c4 Mon Sep 17 00:00:00 2001 From: Changlin Date: Fri, 28 Jun 2024 00:16:48 +0000 Subject: [PATCH 23/34] fix current_source None issue, improve linting --- cwltool/cwlprov/provenance_profile.py | 2 +- cwltool/cwlprov/ro.py | 29 +++++++++++++++++---------- 2 files changed, 19 insertions(+), 12 deletions(-) diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index f5ca8e32d..42ab9e54c 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -657,7 +657,7 @@ def used_artefacts( job_order: Union[CWLObjectType, List[CWLObjectType]], process_run_id: str, name: Optional[str] = None, - load_listing=None, + # load_listing=None, ) -> None: """Add used() for each data artefact.""" if isinstance(job_order, list): diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index b0e39b994..eabf7cdb7 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -1,7 +1,7 @@ """Stores class definition of ResearchObject and WritableBagFile.""" import datetime -import hashlib +# import hashlib import os import shutil import tempfile @@ -364,6 +364,7 @@ def guess_mediatype( def add_uri( self, uri: str, timestamp: Optional[datetime.datetime] = None ) -> Aggregate: + """Add external URI to the Research Object.""" self.self_check() aggr: Aggregate = {"uri": uri} aggr["createdOn"], aggr["createdBy"] = self._self_made(timestamp=timestamp) @@ -501,7 +502,7 @@ def has_data_file(self, location: str, sha1hash: str) -> bool: def add_data_file( self, from_fp: IO[Any], - current_source: str = None, # source/destination of the incoming file, e.g. "data/input" or "data/output" + current_source: str = INPUT_DATA, # source/destination of the incoming file, e.g. "data/input" or "data/output" timestamp: Optional[datetime.datetime] = None, content_type: Optional[str] = None, ) -> str: @@ -537,7 +538,7 @@ def add_data_file( rel_path = posix_path(os.path.relpath(path, self.folder)) # Register in bagit checksum - if Hasher == hashlib.sha1: + if Hasher == SHA1: self._add_to_bagit( rel_path, sha1=checksum ) # that is actually saving the file to the prov RO folder @@ -547,13 +548,20 @@ def add_data_file( ) # Inefficient, bagit support need to checksum again self._add_to_bagit(rel_path) - if "dir" in self.relativised_input_object: - _logger.debug( - "[provenance] Directory :%s", - self.relativised_input_object["dir"]["basename"], - ) + # check if self.relativised_input_object is dict + if isinstance(self.relativised_input_object, MutableMapping): + # check if "dir" exist and is a dict + if "dir" in self.relativised_input_object and isinstance(self.relativised_input_object["dir"], MutableMapping): + # now safe to access "basename" key + JustABasename = self.relativised_input_object["dir"]["basename"] + _logger.debug( + "[provenance] Directory :%s", + JustABasename, + ) + else: + _logger.debug("[provenance] Added data file %s", path) else: - _logger.debug("[provenance] Added data file %s", path) + _logger.debug("[provenance] Input CWL object is not indexable") if timestamp is not None: createdOn, createdBy = self._self_made(timestamp) self._file_provenance[rel_path] = cast( @@ -604,12 +612,11 @@ def add_to_manifest(self, rel_path: str, checksums: Dict[str, str]) -> None: checksum_file.write(line) def _add_to_bagit(self, rel_path: str, **checksums: str) -> None: - """ Compute data file size and checksums and adds to bagit manifest. + NOTE: THIS IS WHERE DATAFILE COPYING REALLY HAPPENS WITH checksum_copy """ - if PurePosixPath(rel_path).is_absolute(): raise ValueError(f"rel_path must be relative: {rel_path}") lpath = os.path.join(self.folder, local_path(rel_path)) From b3a85c6f9148e4ef99629805db443394df6aa30c Mon Sep 17 00:00:00 2001 From: Changlin Date: Fri, 28 Jun 2024 00:26:55 +0000 Subject: [PATCH 24/34] docstring fix and lint fix --- cwltool/cwlprov/provenance_profile.py | 15 +++++++++++---- cwltool/cwlprov/ro.py | 15 ++++++++++----- 2 files changed, 21 insertions(+), 9 deletions(-) diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 42ab9e54c..521aedc21 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -688,9 +688,15 @@ def generate_output_prov( process_run_id: Optional[str], name: Optional[str], ) -> None: - """Call wasGeneratedBy() for each output, copy the files into the RO.""" - # To save output data in ro.py add_data_file() method, use a var current_data_source to keep track of whether it's input or output (maybe intermediate in the future) data - # it is later injected to add_data_file() method to save the data in the correct folder, thus avoid changing the provenance_constants DATA + """ + Call wasGeneratedBy() for each output, copy the files into the RO. + + To save output data in ro.py add_data_file() method, + use a var current_data_source to keep track of whether it's + input or output (maybe intermediate in the future) data + it is later injected to add_data_file() method to save the data in the correct folder, + thus avoid changing the provenance_constants DATA + """ self.current_data_source = OUTPUT_DATA if isinstance(final_output, MutableSequence): @@ -794,7 +800,8 @@ def finalize_prov_profile(self, name: Optional[str]) -> List[QualifiedName]: # TODO: Also support other profiles than CWLProv, e.g. ProvOne # list of prov identifiers of provenance files - # prov_ids are file names prepared for provenance/RO files in metadata/provenance for each sub-workflow of main workflow + # NOTE: prov_ids are file names prepared for provenance/RO files in + # metadata/provenance for each sub-workflow of main workflow prov_ids = [] # https://www.w3.org/TR/prov-xml/ diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index eabf7cdb7..b4a1c84df 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -502,11 +502,15 @@ def has_data_file(self, location: str, sha1hash: str) -> bool: def add_data_file( self, from_fp: IO[Any], - current_source: str = INPUT_DATA, # source/destination of the incoming file, e.g. "data/input" or "data/output" + current_source: str = INPUT_DATA, timestamp: Optional[datetime.datetime] = None, content_type: Optional[str] = None, ) -> str: - """Copy data files to data/ folder.""" + """ + Copy data files to data/ folder. + + current_sourcw is the destination of the incoming file, e.g. "data/input" or "data/output" + """ # This also copies the outputs via declare_artefacts -> generate_output_prov # Skip certain files if no-input or no-data is used self.self_check() @@ -551,7 +555,8 @@ def add_data_file( # check if self.relativised_input_object is dict if isinstance(self.relativised_input_object, MutableMapping): # check if "dir" exist and is a dict - if "dir" in self.relativised_input_object and isinstance(self.relativised_input_object["dir"], MutableMapping): + if "dir" in self.relativised_input_object and \ + isinstance(self.relativised_input_object["dir"], MutableMapping): # now safe to access "basename" key JustABasename = self.relativised_input_object["dir"]["basename"] _logger.debug( @@ -614,7 +619,7 @@ def add_to_manifest(self, rel_path: str, checksums: Dict[str, str]) -> None: def _add_to_bagit(self, rel_path: str, **checksums: str) -> None: """ Compute data file size and checksums and adds to bagit manifest. - + NOTE: THIS IS WHERE DATAFILE COPYING REALLY HAPPENS WITH checksum_copy """ if PurePosixPath(rel_path).is_absolute(): @@ -632,7 +637,7 @@ def _add_to_bagit(self, rel_path: str, **checksums: str) -> None: # ensure we always have sha1 checksums = dict(checksums) with open(lpath, "rb") as file_path: - # FIXME: Need sha-256 / sha-512 as well for Research Object BagIt profile? maybe slowing down the process a lot. + # FIXME: Need sha-256 / sha-512 as well for Research Object BagIt profile? if ( self.no_input and os.path.commonprefix([provenance_constants.INPUT_DATA, lpath]) From 7b748de999ee4c12dc8bf763c316b4b019cb15f4 Mon Sep 17 00:00:00 2001 From: Changlin Date: Fri, 28 Jun 2024 00:29:18 +0000 Subject: [PATCH 25/34] remove load_listing param for used_artefacts --- cwltool/job.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cwltool/job.py b/cwltool/job.py index fe7073856..dd10dda1d 100644 --- a/cwltool/job.py +++ b/cwltool/job.py @@ -290,7 +290,7 @@ def _execute( job_order, runtimeContext.process_run_id, str(self.name), - load_listing=self.builder.loadListing, + # load_listing=self.builder.loadListing, ) else: _logger.warning( From a47e73c9fa42a9e7edd60970affcf81f1611270e Mon Sep 17 00:00:00 2001 From: Changlin Date: Fri, 28 Jun 2024 00:38:46 +0000 Subject: [PATCH 26/34] fix lint --- cwltool/cwlprov/provenance_profile.py | 10 +++++----- cwltool/cwlprov/ro.py | 12 ++++++++---- 2 files changed, 13 insertions(+), 9 deletions(-) diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index 521aedc21..fc315aeb0 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -690,11 +690,11 @@ def generate_output_prov( ) -> None: """ Call wasGeneratedBy() for each output, copy the files into the RO. - - To save output data in ro.py add_data_file() method, - use a var current_data_source to keep track of whether it's + + To save output data in ro.py add_data_file() method, + use a var current_data_source to keep track of whether it's input or output (maybe intermediate in the future) data - it is later injected to add_data_file() method to save the data in the correct folder, + it is later injected to add_data_file() method to save the data in the correct folder, thus avoid changing the provenance_constants DATA """ self.current_data_source = OUTPUT_DATA @@ -800,7 +800,7 @@ def finalize_prov_profile(self, name: Optional[str]) -> List[QualifiedName]: # TODO: Also support other profiles than CWLProv, e.g. ProvOne # list of prov identifiers of provenance files - # NOTE: prov_ids are file names prepared for provenance/RO files in + # NOTE: prov_ids are file names prepared for provenance/RO files in # metadata/provenance for each sub-workflow of main workflow prov_ids = [] diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index b4a1c84df..63e3d658c 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -502,13 +502,13 @@ def has_data_file(self, location: str, sha1hash: str) -> bool: def add_data_file( self, from_fp: IO[Any], - current_source: str = INPUT_DATA, + current_source: str = INPUT_DATA, timestamp: Optional[datetime.datetime] = None, content_type: Optional[str] = None, ) -> str: """ Copy data files to data/ folder. - + current_sourcw is the destination of the incoming file, e.g. "data/input" or "data/output" """ # This also copies the outputs via declare_artefacts -> generate_output_prov @@ -556,7 +556,7 @@ def add_data_file( if isinstance(self.relativised_input_object, MutableMapping): # check if "dir" exist and is a dict if "dir" in self.relativised_input_object and \ - isinstance(self.relativised_input_object["dir"], MutableMapping): + isinstance(self.relativised_input_object["dir"], MutableMapping): # now safe to access "basename" key JustABasename = self.relativised_input_object["dir"]["basename"] _logger.debug( @@ -590,7 +590,11 @@ def _self_made( ) def add_to_manifest(self, rel_path: str, checksums: Dict[str, str]) -> None: - """Add files to the research object manifest. Data files are added to manifest regardless of the state of no_data/no_input flag.""" + """ + Add files to the research object manifest. + + Data files are added to manifest regardless of the state of no_data/no_input flag. + """ self.self_check() if PurePosixPath(rel_path).is_absolute(): raise ValueError(f"rel_path must be relative: {rel_path}") From 2acc4c0c6f0faf90c900271da26a06c780227934 Mon Sep 17 00:00:00 2001 From: Changlin Date: Fri, 28 Jun 2024 00:49:39 +0000 Subject: [PATCH 27/34] fix conformity issue --- cwltool/cwlprov/__init__.py | 2 +- cwltool/cwlprov/ro.py | 5 ++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/cwltool/cwlprov/__init__.py b/cwltool/cwlprov/__init__.py index af7ca99c1..fbac64240 100644 --- a/cwltool/cwlprov/__init__.py +++ b/cwltool/cwlprov/__init__.py @@ -168,7 +168,7 @@ def checksum_copy( def checksum_only( src_file: IO[Any], dst_file: Optional[IO[Any]] = None, - hasher: Optional[str] = Hasher, + hasher: str = Hasher, buffersize: int = 1024 * 1024, ) -> str: """Calculate the checksum only, does not copy the data files.""" diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 63e3d658c..0fc4f685d 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -565,8 +565,7 @@ def add_data_file( ) else: _logger.debug("[provenance] Added data file %s", path) - else: - _logger.debug("[provenance] Input CWL object is not indexable") + if timestamp is not None: createdOn, createdBy = self._self_made(timestamp) self._file_provenance[rel_path] = cast( @@ -591,7 +590,7 @@ def _self_made( def add_to_manifest(self, rel_path: str, checksums: Dict[str, str]) -> None: """ - Add files to the research object manifest. + Add files to the research object manifest. Data files are added to manifest regardless of the state of no_data/no_input flag. """ From d6bdc7f0dc81ea7127d3e475d7f7758631691dbf Mon Sep 17 00:00:00 2001 From: Changlin Date: Sat, 29 Jun 2024 21:09:56 +0000 Subject: [PATCH 28/34] run black for uncompromising python code format --- cwltool/cwlprov/provenance_profile.py | 72 +++++++-------------------- cwltool/cwlprov/ro.py | 47 ++++++----------- cwltool/cwlprov/writablebagfile.py | 4 +- 3 files changed, 33 insertions(+), 90 deletions(-) diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py index fc315aeb0..16be3a9ad 100644 --- a/cwltool/cwlprov/provenance_profile.py +++ b/cwltool/cwlprov/provenance_profile.py @@ -60,9 +60,7 @@ from .ro import ResearchObject -def copy_job_order( - job: Union[Process, JobsType], job_order_object: CWLObjectType -) -> CWLObjectType: +def copy_job_order(job: Union[Process, JobsType], job_order_object: CWLObjectType) -> CWLObjectType: """Create copy of job object for provenance.""" if not isinstance(job, WorkflowJob): # direct command line tool execution @@ -124,9 +122,7 @@ def __init__( def __str__(self) -> str: """Represent this Provenvance profile as a string.""" - return ( - f"ProvenanceProfile <{self.workflow_run_uri}> in <{self.research_object}>" - ) + return f"ProvenanceProfile <{self.workflow_run_uri}> in <{self.research_object}>" def generate_prov_doc(self) -> Tuple[str, ProvDocument]: """Generate a provenance document. @@ -187,9 +183,7 @@ def host_provenance(document: ProvDocument) -> None: ) ro_identifier_workflow = self.research_object.base_uri + "workflow/packed.cwl#" self.wf_ns = self.document.add_namespace("wf", ro_identifier_workflow) - ro_identifier_input = ( - self.research_object.base_uri + "workflow/primary-job.json#" - ) + ro_identifier_input = self.research_object.base_uri + "workflow/primary-job.json#" self.document.add_namespace("input", ro_identifier_input) # More info about the account (e.g. username, fullname) @@ -240,9 +234,7 @@ def host_provenance(document: ProvDocument) -> None: ) # association between SoftwareAgent and WorkflowRun main_workflow = "wf:main" - self.document.wasAssociatedWith( - self.workflow_run_uri, self.engine_uuid, main_workflow - ) + self.document.wasAssociatedWith(self.workflow_run_uri, self.engine_uuid, main_workflow) self.document.wasStartedBy( self.workflow_run_uri, None, self.engine_uuid, datetime.datetime.now() ) @@ -301,9 +293,7 @@ def start_process( self.document.wasAssociatedWith( process_run_id, self.engine_uuid, str("wf:main/" + process_name) ) - self.document.wasStartedBy( - process_run_id, None, self.workflow_run_uri, when, None, None - ) + self.document.wasStartedBy(process_run_id, None, self.workflow_run_uri, when, None, None) return process_run_id def record_process_end( @@ -341,9 +331,7 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st ) # FIXME: This naively relies on add_data_file setting hash as filename checksum = PurePath(relative_path).name - entity = self.document.entity( - "data:" + checksum, {PROV_TYPE: WFPROV["Artifact"]} - ) + entity = self.document.entity("data:" + checksum, {PROV_TYPE: WFPROV["Artifact"]}) if "checksum" not in value: value["checksum"] = f"{SHA1}${checksum}" @@ -353,9 +341,7 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st # By here one of them should have worked! if not entity or not checksum: - raise ValueError( - "class:File but missing checksum/location/content: %r" % value - ) + raise ValueError("class:File but missing checksum/location/content: %r" % value) # Track filename and extension, this is generally useful only for # secondaryFiles. Note that multiple uses of a file might thus record @@ -369,23 +355,15 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st ) if "basename" in value: - file_entity.add_attributes( - {CWLPROV["basename"]: cast(str, value["basename"])} - ) + file_entity.add_attributes({CWLPROV["basename"]: cast(str, value["basename"])}) if "nameroot" in value: - file_entity.add_attributes( - {CWLPROV["nameroot"]: cast(str, value["nameroot"])} - ) + file_entity.add_attributes({CWLPROV["nameroot"]: cast(str, value["nameroot"])}) if "nameext" in value: - file_entity.add_attributes( - {CWLPROV["nameext"]: cast(str, value["nameext"])} - ) + file_entity.add_attributes({CWLPROV["nameext"]: cast(str, value["nameext"])}) self.document.specializationOf(file_entity, entity) # Check for secondaries - for sec in cast( - MutableSequence[CWLObjectType], value.get("secondaryFiles", []) - ): + for sec in cast(MutableSequence[CWLObjectType], value.get("secondaryFiles", [])): # TODO: Record these in a specializationOf entity with UUID? if sec["class"] == "File": (sec_entity, _, _) = self.declare_file(sec) @@ -505,9 +483,7 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: ore_doc_path = str(PurePosixPath(METADATA, ore_doc_fn)) with write_bag_file(self.research_object, ore_doc_path) as provenance_file: ore_doc.serialize(provenance_file, format="rdf", rdf_format="turtle") - self.research_object.add_annotation( - dir_id, [ore_doc_fn], ORE["isDescribedBy"].uri - ) + self.research_object.add_annotation(dir_id, [ore_doc_fn], ORE["isDescribedBy"].uri) if is_empty: # Empty directory @@ -609,9 +585,7 @@ def declare_artefact(self, value: Any) -> ProvEntity: # https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition # as prov.py do not easily allow PROV-N extensions m_entity.add_asserted_type(PROV["KeyEntityPair"]) - m_entity.add_attributes( - {PROV["pairKey"]: str(key), PROV["pairEntity"]: v_ent} - ) + m_entity.add_attributes({PROV["pairKey"]: str(key), PROV["pairEntity"]: v_ent}) coll_attribs.append((PROV["hadDictionaryMember"], m_entity)) coll.add_attributes(coll_attribs) self.research_object.add_uri(coll.identifier.uri) @@ -765,9 +739,7 @@ def prospective_prov(self, job: JobsType) -> None: ) # TODO: Declare roles/parameters as well - def activity_has_provenance( - self, activity: str, prov_ids: Sequence[Identifier] - ) -> None: + def activity_has_provenance(self, activity: str, prov_ids: Sequence[Identifier]) -> None: """Add http://www.w3.org/TR/prov-aq/ relations to nested PROV files.""" # NOTE: The below will only work if the corresponding metadata/provenance arcp URI # is a pre-registered namespace in the PROV Document @@ -810,16 +782,12 @@ def finalize_prov_profile(self, name: Optional[str]) -> List[QualifiedName]: prov_ids.append(self.provenance_ns[filename + ".xml"]) # https://www.w3.org/TR/prov-n/ - with write_bag_file( - self.research_object, basename + ".provn" - ) as provenance_file: + with write_bag_file(self.research_object, basename + ".provn") as provenance_file: self.document.serialize(provenance_file, format="provn", indent=2) prov_ids.append(self.provenance_ns[filename + ".provn"]) # https://www.w3.org/Submission/prov-json/ - with write_bag_file( - self.research_object, basename + ".json" - ) as provenance_file: + with write_bag_file(self.research_object, basename + ".json") as provenance_file: self.document.serialize(provenance_file, format="json", indent=2) prov_ids.append(self.provenance_ns[filename + ".json"]) @@ -833,18 +801,14 @@ def finalize_prov_profile(self, name: Optional[str]) -> List[QualifiedName]: # https://www.w3.org/TR/n-triples/ with write_bag_file(self.research_object, basename + ".nt") as provenance_file: - self.document.serialize( - provenance_file, format="rdf", rdf_format="ntriples" - ) + self.document.serialize(provenance_file, format="rdf", rdf_format="ntriples") prov_ids.append(self.provenance_ns[filename + ".nt"]) # https://www.w3.org/TR/json-ld/ # TODO: Use a nice JSON-LD context # see also https://eprints.soton.ac.uk/395985/ # 404 Not Found on https://provenance.ecs.soton.ac.uk/prov.jsonld :( - with write_bag_file( - self.research_object, basename + ".jsonld" - ) as provenance_file: + with write_bag_file(self.research_object, basename + ".jsonld") as provenance_file: self.document.serialize(provenance_file, format="rdf", rdf_format="json-ld") prov_ids.append(self.provenance_ns[filename + ".jsonld"]) diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 0fc4f685d..8e2726be2 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -1,6 +1,7 @@ """Stores class definition of ResearchObject and WritableBagFile.""" import datetime + # import hashlib import os import shutil @@ -184,9 +185,7 @@ def user_provenance(self, document: ProvDocument) -> None: # get their name wrong!) document.actedOnBehalfOf(account, user) - def add_tagfile( - self, path: str, timestamp: Optional[datetime.datetime] = None - ) -> None: + def add_tagfile(self, path: str, timestamp: Optional[datetime.datetime] = None) -> None: """Add tag files to our research object.""" self.self_check() checksums = {} @@ -263,16 +262,11 @@ def guess_mediatype( extension = None mediatype: Optional[str] = media_types.get(extension, None) - conformsTo: Optional[Union[str, List[str]]] = conforms_to.get( - extension, None - ) + conformsTo: Optional[Union[str, List[str]]] = conforms_to.get(extension, None) # TODO: Open CWL file to read its declared "cwlVersion", e.g. # cwlVersion = "v1.0" - if ( - rel_path.startswith(posix_path(PROVENANCE)) - and extension in prov_conforms_to - ): + if rel_path.startswith(posix_path(PROVENANCE)) and extension in prov_conforms_to: if ".cwlprov" in rel_path: # Our own! conformsTo = [ @@ -327,9 +321,7 @@ def guess_mediatype( for path in self.tagfiles: if not ( - path.startswith(METADATA) - or path.startswith(WORKFLOW) - or path.startswith(SNAPSHOT) + path.startswith(METADATA) or path.startswith(WORKFLOW) or path.startswith(SNAPSHOT) ): # probably a bagit file continue @@ -361,9 +353,7 @@ def guess_mediatype( aggregates.extend(self._external_aggregates) return aggregates - def add_uri( - self, uri: str, timestamp: Optional[datetime.datetime] = None - ) -> Aggregate: + def add_uri(self, uri: str, timestamp: Optional[datetime.datetime] = None) -> Aggregate: """Add external URI to the Research Object.""" self.self_check() aggr: Aggregate = {"uri": uri} @@ -478,12 +468,8 @@ def generate_snapshot(self, prov_dep: CWLObjectType) -> None: shutil.copytree(filepath, path) else: shutil.copy(filepath, path) - timestamp = datetime.datetime.fromtimestamp( - os.path.getmtime(filepath) - ) - self.add_tagfile( - path, timestamp - ) # add snapshots as tag files to the RO + timestamp = datetime.datetime.fromtimestamp(os.path.getmtime(filepath)) + self.add_tagfile(path, timestamp) # add snapshots as tag files to the RO except PermissionError: pass # FIXME: avoids duplicate snapshotting; need better solution elif key in ("secondaryFiles", "listing"): @@ -524,9 +510,7 @@ def add_data_file( rel_path = posix_path(os.path.relpath(path, self.folder)) else: # calculate checksum and copy file to a tmp location - with tempfile.NamedTemporaryFile( - prefix=tmp_prefix, dir=tmp_dir, delete=False - ) as tmp: + with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp: checksum = checksum_copy(from_fp, tmp) folder = os.path.join(self.folder, current_source, checksum[0:2]) path = os.path.join(folder, checksum) @@ -555,8 +539,9 @@ def add_data_file( # check if self.relativised_input_object is dict if isinstance(self.relativised_input_object, MutableMapping): # check if "dir" exist and is a dict - if "dir" in self.relativised_input_object and \ - isinstance(self.relativised_input_object["dir"], MutableMapping): + if "dir" in self.relativised_input_object and isinstance( + self.relativised_input_object["dir"], MutableMapping + ): # now safe to access "basename" key JustABasename = self.relativised_input_object["dir"]["basename"] _logger.debug( @@ -612,9 +597,7 @@ def add_to_manifest(self, rel_path: str, checksums: Dict[str, str]) -> None: # existence in bagged_size above manifestpath = os.path.join(self.folder, f"{manifest}-{method.lower()}.txt") # encoding: match Tag-File-Character-Encoding: UTF-8 - with open( - manifestpath, "a", encoding=ENCODING, newline="\n" - ) as checksum_file: + with open(manifestpath, "a", encoding=ENCODING, newline="\n") as checksum_file: line = f"{hash_value} {rel_path}\n" _logger.debug("[provenance] Added to %s: %s", manifestpath, line) checksum_file.write(line) @@ -685,9 +668,7 @@ def _relativise_files( structure["basename"], structure["location"], ) - with self.fsaccess.open( - cast(str, structure["location"]), "rb" - ) as fp: + with self.fsaccess.open(cast(str, structure["location"]), "rb") as fp: relative_path = self.add_data_file(fp) checksum = PurePosixPath(relative_path).name structure["checksum"] = f"{SHA1}${checksum}" diff --git a/cwltool/cwlprov/writablebagfile.py b/cwltool/cwlprov/writablebagfile.py index e0ca4f76b..313c87120 100644 --- a/cwltool/cwlprov/writablebagfile.py +++ b/cwltool/cwlprov/writablebagfile.py @@ -46,9 +46,7 @@ def __init__(self, research_object: "ResearchObject", rel_path: str) -> None: SHA512: hashlib.sha512(), } # Open file in Research Object folder - path = os.path.abspath( - os.path.join(research_object.folder, local_path(rel_path)) - ) + path = os.path.abspath(os.path.join(research_object.folder, local_path(rel_path))) if not path.startswith(os.path.abspath(research_object.folder)): raise ValueError("Path is outside Research Object: %s" % path) _logger.debug("[provenance] Creating WritableBagFile at %s.", path) From 0a17526115dbbdd7fd8c6c843afff774f0033e86 Mon Sep 17 00:00:00 2001 From: Changlin Date: Sun, 30 Jun 2024 01:59:51 +0000 Subject: [PATCH 29/34] fix no_input --- cwltool/cwlprov/ro.py | 3 ++- tests/test_provenance.py | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 8e2726be2..9fc1d93ff 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -626,10 +626,11 @@ def _add_to_bagit(self, rel_path: str, **checksums: str) -> None: # FIXME: Need sha-256 / sha-512 as well for Research Object BagIt profile? if ( self.no_input - and os.path.commonprefix([provenance_constants.INPUT_DATA, lpath]) + and os.path.commonprefix([provenance_constants.INPUT_DATA, rel_path]) == provenance_constants.INPUT_DATA ): checksums[SHA1] = checksum_only(file_path, hasher=SHA1) + _logger.debug(f"[provenance] No input - skipped copying: {rel_path}") else: checksums[SHA1] = checksum_copy(file_path, hasher=SHA1) diff --git a/tests/test_provenance.py b/tests/test_provenance.py index f06be3c20..7ed8ee163 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -860,7 +860,7 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: p = folder / "data" / "input" / prefix / file_hash # File should be empty and in the future not existing... # assert os.path.getsize(p.absolute()) == 0 - # To be discared when file really does not exist anymore + # To be discared, discard when file really does not exist anymore if f in ["d", "e", "f", "g", "h", "i"]: print(f"Analysing file {f}") assert not p.is_file(), f"Could find {f} as {p}" From fe04191958d732c215f955127ab03fe9eab80935 Mon Sep 17 00:00:00 2001 From: Changlin Date: Sun, 30 Jun 2024 16:11:06 +0000 Subject: [PATCH 30/34] black format fix --- cwlref-runner/setup.py | 31 ++++++++++++++----------------- cwltool/cwlprov/ro.py | 8 ++++++++ docs/conf.py | 1 + 3 files changed, 23 insertions(+), 17 deletions(-) diff --git a/cwlref-runner/setup.py b/cwlref-runner/setup.py index 98db70e36..1f6e4a914 100644 --- a/cwlref-runner/setup.py +++ b/cwlref-runner/setup.py @@ -4,22 +4,19 @@ from setuptools import setup, find_packages SETUP_DIR = os.path.dirname(__file__) -README = os.path.join(SETUP_DIR, 'README') +README = os.path.join(SETUP_DIR, "README") -setup(name='cwlref-runner', - version='1.0', - description='Common workflow language reference implementation', - long_description=open(README).read(), - author='Common workflow language working group', - author_email='common-workflow-language@googlegroups.com', - url="http://www.commonwl.org", - download_url="https://github.com/common-workflow-language/common-workflow-language", - license='Apache 2.0', - install_requires=[ - 'cwltool' - ], - entry_points={ - 'console_scripts': [ "cwl-runner=cwltool.main:main" ] - }, - zip_safe=True +setup( + name="cwlref-runner", + version="1.0", + description="Common workflow language reference implementation", + long_description=open(README).read(), + author="Common workflow language working group", + author_email="common-workflow-language@googlegroups.com", + url="http://www.commonwl.org", + download_url="https://github.com/common-workflow-language/common-workflow-language", + license="Apache 2.0", + install_requires=["cwltool"], + entry_points={"console_scripts": ["cwl-runner=cwltool.main:main"]}, + zip_safe=True, ) diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py index 9fc1d93ff..1c2df9591 100644 --- a/cwltool/cwlprov/ro.py +++ b/cwltool/cwlprov/ro.py @@ -508,6 +508,14 @@ def add_data_file( path = os.path.join(folder, checksum) # Relative posix path rel_path = posix_path(os.path.relpath(path, self.folder)) + elif self.no_input and current_source == INPUT_DATA: + # for now do the same as no_data when no_input is used for input files + checksum = checksum_only(from_fp) + # Create rel_path + folder = os.path.join(self.folder, current_source, checksum[0:2]) + path = os.path.join(folder, checksum) + # Relative posix path + rel_path = posix_path(os.path.relpath(path, self.folder)) else: # calculate checksum and copy file to a tmp location with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp: diff --git a/docs/conf.py b/docs/conf.py index 6e04b5d64..4be78f80f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -7,6 +7,7 @@ # -- Path setup -------------------------------------------------------------- import importlib.metadata + # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. From 6b060756325aefe8427b4fae4427df2f77f8f75a Mon Sep 17 00:00:00 2001 From: Changlin Date: Mon, 1 Jul 2024 13:24:49 +0000 Subject: [PATCH 31/34] typo fix --- tests/test_provenance.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_provenance.py b/tests/test_provenance.py index 7ed8ee163..7524298a4 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -860,7 +860,7 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: p = folder / "data" / "input" / prefix / file_hash # File should be empty and in the future not existing... # assert os.path.getsize(p.absolute()) == 0 - # To be discared, discard when file really does not exist anymore + # To be discarded when file really does not exist anymore if f in ["d", "e", "f", "g", "h", "i"]: print(f"Analysing file {f}") assert not p.is_file(), f"Could find {f} as {p}" From 4d41ca41a33cfdbe2ef1fe42b2f7766a261f0f62 Mon Sep 17 00:00:00 2001 From: Changlin Date: Wed, 3 Jul 2024 13:29:37 +0000 Subject: [PATCH 32/34] fix typing hint in test_provenance.py --- tests/test_provenance.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/test_provenance.py b/tests/test_provenance.py index 7524298a4..ec864f844 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -4,7 +4,7 @@ import sys import urllib from pathlib import Path -from typing import IO, Any, Generator, cast +from typing import IO, Any, Generator, cast, Tuple, Dict import arcp import bagit @@ -795,7 +795,7 @@ def test_research_object_picklability(research_object: ResearchObject) -> None: # Function to list filestructure -def list_files(startpath): +def list_files(startpath: Path) -> None: startpath = str(startpath) print("Root: ", startpath) for root, _dirs, files in os.walk(startpath): @@ -869,7 +869,7 @@ def test_directory_workflow_no_listing(tmp_path: Path) -> None: assert p.is_file(), f"Could not find {f} as {p}" -def prepare_input_files(tmp_path: Path) -> None: +def prepare_input_files(tmp_path: Path) -> Tuple[Dict[str, str], Path, Path, Path]: sha1 = { # Expected hashes of ASCII letters (no linefeed) # as returned from: From f1445e07caad4c2dd2cc6a34e034cd2684321949 Mon Sep 17 00:00:00 2001 From: Changlin Date: Tue, 9 Jul 2024 14:14:19 +0200 Subject: [PATCH 33/34] improve cwlview viz for large workflow --- cwltool/cwlviewer.py | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/cwltool/cwlviewer.py b/cwltool/cwlviewer.py index e544a568e..24eccc17c 100644 --- a/cwltool/cwlviewer.py +++ b/cwltool/cwlviewer.py @@ -64,6 +64,12 @@ def _set_inner_edges(self) -> None: ) n.set_name(str(inner_edge_row["source_step"])) self._dot_graph.add_node(n) + + # Add the edge with a label specifying the output and input files + edge_from_output_of = urlparse(inner_edge_row["output_ref"]).fragment + edge_to_input_of = urlparse(inner_edge_row["target_ref_input"]).fragment + edge_label = f"{edge_from_output_of} -> {edge_to_input_of}" + target_label = ( inner_edge_row["target_label"] if inner_edge_row["target_label"] is not None @@ -91,6 +97,11 @@ def _set_inner_edges(self) -> None: pydot.Edge( str(inner_edge_row["source_step"]), str(inner_edge_row["target_step"]), + label=edge_label, + fontsize="10", # set the font size for edge labels + fontcolor="blue", # set the font color for edge labels + color="black", # set the edge color + arrowsize="0.7" # set the arrow size ) ) @@ -175,8 +186,29 @@ def _init_dot_graph(cls) -> pydot.Graph: graph.set("bgcolor", "#eeeeee") graph.set("clusterrank", "local") graph.set("labelloc", "bottom") - graph.set("labelloc", "bottom") graph.set("labeljust", "right") + graph.set("nodesep", "0.75") # Increase the space between nodes + graph.set("ranksep", "1.25") # Increase the space between ranks + graph.set("splines", "true") # Use smooth splines for edges + + # Additional styling for nodes + graph.set_node_defaults( + style="filled", + fillcolor="lightgrey", + shape="box", + fontname="Helvetica", + fontsize="14", + margin="0.2,0.1" + ) + + # Additional styling for edges + graph.set_edge_defaults( + color="black", + arrowhead="normal", + fontname="Helvetica", + fontsize="10", + fontcolor="blue" + ) return graph From b3d9e1985635b7d6c8dd16179f1adb34b9183b4b Mon Sep 17 00:00:00 2001 From: Changlin Ke Date: Mon, 22 Jul 2024 11:57:56 +0200 Subject: [PATCH 34/34] Update tests/test_provenance.py Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com> --- tests/test_provenance.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_provenance.py b/tests/test_provenance.py index ec864f844..2f0359ae6 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -976,8 +976,8 @@ def test_directory_workflow_no_listing_no_input(tmp_path: Path) -> None: if p.is_file(): print(f"Analysing file {f!r} {p!r}") - with open(p, "r", encoding="ascii") as f: - content = f.read() + with open(p, "r", encoding="ascii") as fh: + content = fh.read() print(f"Content: {content!r}") assert not p.is_file(), f"Could find {f!r} as {p!r}" else: